2YWH | pdb_00002ywh

Crystal structure of GDP-bound LepA from Aquifex aeolicus

PDB DOI: https://doi.org/10.2210/pdb2YWH/pdb

Classification: TRANSLATION
Organism(s): Aquifex aeolicus VF5
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2007-04-20 Released: 2008-04-29
Deposition Author(s): Kawazoe, M., Takemoto, C., Kaminishi, T., Nishino, A., Nakayama-Ushikoshi, R., Hanawa-Suetsugu, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free:
0.262 (Depositor), 0.261 (DCC)
R-Value Work:
0.227 (Depositor), 0.227 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal structures of GTP-binding protein LepA from Aquifex aeolicus.

Kawazoe, M., Takemoto, C., Kaminishi, T., Nishino, A., Nakayama-Ushikoshi, R., Hanawa-Suetsugu, K., Terada, T., Shirouzu, M., Yokoyama, S.

To be published.

Macromolecule Content

Total Structure Weight: 68.22 kDa
Atom Count: 4,322
Modeled Residue Count: 528
Deposited Residue Count: 600
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GTP-binding protein LepA	A	600	Aquifex aeolicus VF5	Mutation(s): 0 Gene Names: aq_1725
UniProt
Find proteins for O67618 (Aquifex aeolicus (strain VF5)) Explore O67618 Go to UniProtKB: O67618
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O67618
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GDP Query on GDP 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]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.262 (Depositor), 0.261 (DCC)
R-Value Work: 0.227 (Depositor), 0.227 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.676	α = 90
b = 116.118	β = 90
c = 122.721	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2008-04-29

Deposition Author(s):

Nakayama-Ushikoshi, R.

RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History (Full details and data files)

Version 1.0: 2008-04-29
Type: Initial release
Version 1.1: 2011-07-13
Changes: Source and taxonomy, Version format compliance
Version 1.2: 2017-10-11
Changes: Refinement description
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description