2YWG | pdb_00002ywg

Crystal structure of GTP-bound LepA from Aquifex aeolicus

PDB DOI: https://doi.org/10.2210/pdb2YWG/pdb

Classification: TRANSLATION
Organism(s): Aquifex aeolicus VF5
Expression System: Escherichia coli
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: 2.94 Å
R-Value Free:
0.265 (Depositor), 0.258 (DCC)
R-Value Work:
0.205 (Depositor), 0.203 (DCC)
R-Value Observed:
0.205 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 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: 68.88 kDa
Atom Count: 4,243
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP Query on GTP 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]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.94 Å
R-Value Free: 0.265 (Depositor), 0.258 (DCC)
R-Value Work: 0.205 (Depositor), 0.203 (DCC)
R-Value Observed: 0.205 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.518	α = 90
b = 116.348	β = 90
c = 122.826	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
Version 1.4: 2023-11-15
Changes: Data collection
Version 1.5: 2024-10-30
Changes: Structure summary