2PG4 | pdb_00002pg4

Crystal structure of a putative dna binding protein (ape_0880a) from aeropyrum pernix k1 at 2.21 A resolution

PDB DOI: https://doi.org/10.2210/pdb2PG4/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Aeropyrum pernix K1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2007-04-06 Released: 2007-04-24
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free:
0.258 (Depositor), 0.263 (DCC)
R-Value Work:
0.198 (Depositor), 0.198 (DCC)
R-Value Observed:
0.201 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of uncharacterized protein (NP_147569.1) from Aeropyrum pernix at 2.21 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 22.69 kDa
Atom Count: 1,591
Modeled Residue Count: 183
Deposited Residue Count: 190
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Uncharacterized protein	A, B	95	Aeropyrum pernix K1	Mutation(s): 2 Gene Names: NP_147569.1, APE0880.1, APES039, APE_0880a
UniProt
Find proteins for Q9YDN4 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1)) Explore Q9YDN4 Go to UniProtKB: Q9YDN4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9YDN4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CIT Query on CIT Download:Ideal Coordinates CCD File SDF format, chain K [auth B] MOL2 format, chain K [auth B] mmCIF format, chain K [auth B]	K [auth B]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain K [auth B] Interactions & Density Focus chain K [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain N [auth B] MOL2 format, chain N [auth B] mmCIF format, chain N [auth B]	N [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain N [auth B] Interactions & Density Focus chain N [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], L [auth B], M [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain C [auth A]	C [auth A], I [auth B], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain C [auth A] Focus chain I [auth B] Focus chain J [auth B] Interactions & Density Focus chain C [auth A] Focus chain I [auth B] Focus chain J [auth B]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.21 Å
R-Value Free: 0.258 (Depositor), 0.263 (DCC)
R-Value Work: 0.198 (Depositor), 0.198 (DCC)
R-Value Observed: 0.201 (Depositor)

Diffraction Data:

Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.84	α = 90
b = 109.84	β = 90
c = 36.76	γ = 90

Software Package:

Software Name	Purpose
MolProbity	model building
SHELX	phasing
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
SHARP	phasing

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2007-04-24

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

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: Advisory, Source and taxonomy, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 1.4: 2023-01-25
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Refinement description, Structure summary

2PG4 | pdb_00002pg4

Crystal structure of a putative dna binding protein (ape_0880a) from aeropyrum pernix k1 at 2.21 A resolution

Literature

Crystal structure of uncharacterized protein (NP_147569.1) from Aeropyrum pernix at 2.21 A resolution

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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