3LW7 | pdb_00003lw7

The Crystal Structure of an Adenylate kinase-related protein bound to AMP from sulfolobus solfataricus to 2.3A

PDB DOI: https://doi.org/10.2210/pdb3LW7/pdb

Classification: TRANSFERASE
Organism(s): Saccharolobus solfataricus 98/2
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2010-02-23 Released: 2010-03-09
Deposition Author(s): Stein, A.J., Sather, A., Hendricks, R., Abdullah, J., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.247 (Depositor), 0.240 (DCC)
R-Value Work:
0.206 (Depositor)
R-Value Observed:
0.208 (Depositor)

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Ligand Structure Quality Assessment

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

Literature

The Crystal Structure of an Adenylate kinase-related protein bound to AMP from sulfolobus solfataricus to 2.3A

Stein, A.J., Sather, A., Hendricks, R., Abdullah, J., Joachimiak, A.

To be published.

Macromolecule Content

Total Structure Weight: 41.46 kDa
Atom Count: 2,743
Modeled Residue Count: 340
Deposited Residue Count: 358
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Adenylate kinase related protein (AdkA-like)	A, B	179	Saccharolobus solfataricus 98/2	Mutation(s): 0 Gene Names: SSO1041, Ssol_2012
UniProt
Find proteins for Q97Z90 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2)) Explore Q97Z90 Go to UniProtKB: Q97Z90
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q97Z90
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
AMP Query on AMP Download:Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	ADENOSINE MONOPHOSPHATE C₁₀ H₁₄ N₅ O₇ P UDMBCSSLTHHNCD-KQYNXXCUSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.247 (Depositor), 0.240 (DCC)
R-Value Work: 0.206 (Depositor)
R-Value Observed: 0.208 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.876	α = 90
b = 65.876	β = 90
c = 206.239	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2010-03-09

Deposition Author(s):

Midwest Center for Structural Genomics (MCSG)

Revision History (Full details and data files)

Version 1.0: 2010-03-09
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description
Version 1.3: 2024-02-21
Changes: Data collection, Database references, Derived calculations

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.