1HKQ | pdb_00001hkq

PPS10 plasmid DNA replication initiator protein RepA. Replication inactive, dimeric N-terminal domain.

PDB DOI: https://doi.org/10.2210/pdb1HKQ/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Pseudomonas savastanoi
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2003-03-11 Released: 2003-05-29
Deposition Author(s): Giraldo, R., Fernandez-Tornero, C., Evans, P.R., Diaz-Orejas, R., Romero, A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.272 (Depositor), 0.304 (DCC)
R-Value Work:
0.238 (Depositor)
R-Value Observed:
0.238 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.6 of the entry. See complete history.

Literature

A Conformational Switch between Transcriptional Repression and Replication Initiation in Repa Dimerization Domain

Giraldo, R., Fernandez-Tornero, C., Evans, P.R., Diaz-Orejas, R., Romero, A.

(2003) Nat Struct Biol 10: 496

PubMed: 12825085 Search on PubMed
DOI: https://doi.org/10.1038/nsb0703-496
Primary Citation Related Structures:
1HKQ

Macromolecule Content

Total Structure Weight: 32.31 kDa
Atom Count: 2,087
Modeled Residue Count: 250
Deposited Residue Count: 264
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REPLICATION PROTEIN	A, B	132	Pseudomonas savastanoi	Mutation(s): 0
UniProt
Find proteins for Q52546 (Pseudomonas syringae) Explore Q52546 Go to UniProtKB: Q52546
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q52546
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HG Query on HG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain C [auth A]	C [auth A] E [auth A] F [auth A] G [auth A] I [auth B] C [auth A], E [auth A], F [auth A], G [auth A], I [auth B], K [auth B], L [auth B], M [auth B]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain M [auth B]
BEZ Query on BEZ Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain D [auth A] MOL2 format, chain J [auth B] MOL2 format, chain D [auth A] mmCIF format, chain J [auth B] mmCIF format, chain D [auth A]	D [auth A], J [auth B]	BENZOIC ACID C₇ H₆ O₂ WPYMKLBDIGXBTP-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain J [auth B] Interactions & Density Focus chain D [auth A] Focus chain J [auth B]
PO4 Query on PO4 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.272 (Depositor), 0.304 (DCC)
R-Value Work: 0.238 (Depositor)
R-Value Observed: 0.238 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.866	α = 90
b = 55.533	β = 90
c = 96.073	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing
SHARP	phasing
CNS	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2003-05-29

Deposition Author(s):

Giraldo, R.

Fernandez-Tornero, C.

Evans, P.R.

Diaz-Orejas, R.

Romero, A.

Revision History (Full details and data files)

Version 1.0: 2003-05-29
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-02-27
Changes: Data collection, Experimental preparation, Other
Version 1.4: 2019-04-10
Changes: Data collection, Source and taxonomy
Version 1.5: 2019-07-24
Changes: Data collection
Version 1.6: 2024-05-08
Changes: Data collection, Database references, Derived calculations, Other

1HKQ | pdb_00001hkq

PPS10 plasmid DNA replication initiator protein RepA. Replication inactive, dimeric N-terminal domain.

Literature

A Conformational Switch between Transcriptional Repression and Replication Initiation in Repa Dimerization Domain

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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