9BBO | pdb_00009bbo

Proline utilization A complexed with the product L-glutamate in the aldehyde dehydrogenase active site

PDB DOI: https://doi.org/10.2210/pdb9BBO/pdb

Classification: OXIDOREDUCTASE
Organism(s): Sinorhizobium meliloti
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-04-06 Released: 2025-03-12
Deposition Author(s): Tanner, J.J.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.191 (Depositor), 0.191 (DCC)
R-Value Work:
0.169 (Depositor), 0.169 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Visualization of transient states and molecular motions in the catalytic cycle of the proline catabolic bifunctional enzyme Proline Utilization A from kinetic crystallography and molecular dynamics simulations

Buckley, D.B., Gamage, T., Campbell, A.C., Becker, D.F., Tanner, J.J.

To be published.

Macromolecule Content

Total Structure Weight: 267.06 kDa
Atom Count: 20,529
Modelled Residue Count: 2,437
Deposited Residue Count: 2,470
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Trifunctional transcriptional regulator/proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase	A, B	1,235	Sinorhizobium meliloti	Mutation(s): 0 Gene Names: putA, GHK55_27665
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain R [auth B] SDF format, chain J [auth A] MOL2 format, chain R [auth B] MOL2 format, chain J [auth A] mmCIF format, chain R [auth B] mmCIF format, chain J [auth A]	J [auth A], R [auth B]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain J [auth A] Focus chain R [auth B] Interactions & Density Focus chain J [auth A] Focus chain R [auth B]
PGE Query on PGE Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B]	I [auth A], Q [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain Q [auth B] Interactions & Density Focus chain I [auth A] Focus chain Q [auth B]
GGL (Subject of Investigation/LOI) Query on GGL Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain K [auth B] MOL2 format, chain C [auth A] MOL2 format, chain K [auth B] mmCIF format, chain C [auth A] mmCIF format, chain K [auth B]	C [auth A], K [auth B]	GAMMA-L-GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain C [auth A] Focus chain K [auth B] Interactions & Density Focus chain C [auth A] Focus chain K [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain D [auth A] SDF format, chain H [auth A] SDF format, chain M [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain D [auth A] MOL2 format, chain H [auth A] MOL2 format, chain M [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain D [auth A] mmCIF format, chain H [auth A] mmCIF format, chain M [auth B]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain O [auth B]