3PIT | pdb_00003pit

Crystal structure of M-RasD41E in complex with GppNHp (type 2)

PDB DOI: https://doi.org/10.2210/pdb3PIT/pdb

Classification: SIGNALING PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-11-08 Released: 2011-03-09
Deposition Author(s): Muraoka, S., Matsumoto, K., Shima, F., Hu, L., Ijiri, Y., Hirai, R., Liao, J., Kataoka, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.213 (Depositor), 0.210 (DCC)
R-Value Work:
0.185 (Depositor), 0.180 (DCC)
R-Value Observed:
0.186 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of M-RasD41E in complex with GppNHp (type 2)

Muraoka, S., Matsumoto, K., Shima, F., Hu, L., Ijiri, Y., Hirai, R., Liao, J., Kataoka, T.

To be published.

Macromolecule Content

Total Structure Weight: 21.4 kDa
Atom Count: 1,628
Modeled Residue Count: 168
Deposited Residue Count: 183
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein M-Ras	A	183	Mus musculus	Mutation(s): 1 Gene Names: Mras, Xras EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for O08989 (Mus musculus) Explore O08989 Go to UniProtKB: O08989
IMPC: MGI:1100856
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O08989
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP Query on GNP Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.213 (Depositor), 0.210 (DCC)
R-Value Work: 0.185 (Depositor), 0.180 (DCC)
R-Value Observed: 0.186 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.111	α = 90
b = 89.646	β = 90
c = 41.273	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-03-09

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-03-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description

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Crystal structure of M-RasD41E in complex with GppNHp (type 2)

Crystal structure of M-RasD41E in complex with GppNHp (type 2)

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

3PIT | pdb_00003pit