2PH1 | pdb_00002ph1

Crystal structure of nucleotide-binding protein AF2382 from Archaeoglobus fulgidus, Northeast Structural Genomics Target GR165

PDB DOI: https://doi.org/10.2210/pdb2PH1/pdb

Classification: LIGAND BINDING PROTEIN
Organism(s): Archaeoglobus fulgidus DSM 4304
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-04-10 Released: 2007-04-24
Deposition Author(s): Forouhar, F., Abashidze, M., Seetharaman, J., Janjua, H., Fang, Y., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.278 (Depositor), 0.286 (DCC)
R-Value Work:
0.217 (Depositor), 0.222 (DCC)
R-Value Observed:
0.217 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

Crystal structure of nucleotide-binding protein AF2382 from Archaeoglobus fulgidus.

Forouhar, F., Abashidze, M., Seetharaman, J., Janjua, H., Fang, Y., Xiao, R., Liu, J., Baran, M.C., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Macromolecule Content

Total Structure Weight: 29.34 kDa
Atom Count: 1,936
Modeled Residue Count: 247
Deposited Residue Count: 262
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleotide-binding protein	A	262	Archaeoglobus fulgidus DSM 4304	Mutation(s): 8 Gene Names: AF_2382
UniProt
Find proteins for O30288 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)) Explore O30288 Go to UniProtKB: O30288
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O30288
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN 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]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-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: 2.70 Å
R-Value Free: 0.278 (Depositor), 0.286 (DCC)
R-Value Work: 0.217 (Depositor), 0.222 (DCC)
R-Value Observed: 0.217 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.937	α = 90
b = 78.186	β = 90
c = 49.597	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
SnB	phasing
RESOLVE	phasing

Structure Validation

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View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-04-24

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2007-04-24
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary