4QKQ | pdb_00004qkq

RadA from Methanococcus Voltae in complex with copper phthalocyanine tetrasulfonate inhibitor

PDB DOI: https://doi.org/10.2210/pdb4QKQ/pdb

Classification: DNA BINDING PROTEIN
Organism(s): Methanococcus voltae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-06-09 Released: 2015-06-10
Deposition Author(s): Rao, D.E.C.S., Li, Y., He, Y., Luo, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.267 (Depositor), 0.267 (DCC)
R-Value Work:
0.224 (Depositor), 0.225 (DCC)
R-Value Observed:
0.224 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of an archaeal Rad51 homolog in complex with a phthalocyanine tetrasulfonate inhibitor

Rao, D.E.C.S., Li, Y., He, Y., Luo, Y.

To be published.

Macromolecule Content

Total Structure Weight: 354.92 kDa
Atom Count: 24,572
Modeled Residue Count: 3,084
Deposited Residue Count: 3,192
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA repair and recombination protein RadA	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	266	Methanococcus voltae	Mutation(s): 0 Gene Names: radA
UniProt
Find proteins for O73948 (Methanococcus voltae) Explore O73948 Go to UniProtKB: O73948
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O73948
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
35N Query on 35N Download:Ideal Coordinates CCD File SDF format, chain DA [auth G] MOL2 format, chain DA [auth G] mmCIF format, chain DA [auth G]	DA [auth G]	Copper(II) tetrapyrrole C₁₆ H₁₆ Cu N₄ OETWXTGZUZOMCR-UHFFFAOYSA-N		Interactions Focus chain DA [auth G] Interactions & Density Focus chain DA [auth G]
NO3 Query on NO3 Download:Ideal Coordinates CCD File SDF format, chain EA [auth G] SDF format, chain FA [auth G] SDF format, chain JA [auth I] SDF format, chain LA [auth J] SDF format, chain M [auth A] SDF format, chain NA [auth K] SDF format, chain O [auth A] SDF format, chain OA [auth K] SDF format, chain P [auth B] SDF format, chain PA [auth L] SDF format, chain QA [auth L] SDF format, chain T [auth C] SDF format, chain W [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth E] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain S [auth C] SDF format, chain R [auth C] SDF format, chain Q [auth B] SDF format, chain N [auth A] SDF format, chain MA [auth J] SDF format, chain KA [auth I] SDF format, chain IA [auth I] SDF format, chain HA [auth H] SDF format, chain GA [auth H] SDF format, chain CA [auth F] SDF format, chain BA [auth F] SDF format, chain AA [auth F] MOL2 format, chain EA [auth G] MOL2 format, chain FA [auth G] MOL2 format, chain JA [auth I] MOL2 format, chain LA [auth J] MOL2 format, chain M [auth A] MOL2 format, chain NA [auth K] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth K] MOL2 format, chain P [auth B] MOL2 format, chain PA [auth L] MOL2 format, chain QA [auth L] MOL2 format, chain T [auth C] MOL2 format, chain W [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain S [auth C] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth J] MOL2 format, chain KA [auth I] MOL2 format, chain IA [auth I] MOL2 format, chain HA [auth H] MOL2 format, chain GA [auth H] MOL2 format, chain CA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain EA [auth G] mmCIF format, chain FA [auth G] mmCIF format, chain JA [auth I] mmCIF format, chain LA [auth J] mmCIF format, chain M [auth A] mmCIF format, chain NA [auth K] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth K] mmCIF format, chain P [auth B] mmCIF format, chain PA [auth L] mmCIF format, chain QA [auth L] mmCIF format, chain T [auth C] mmCIF format, chain W [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain S [auth C] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth J] mmCIF format, chain KA [auth I] mmCIF format, chain IA [auth I] mmCIF format, chain HA [auth H] mmCIF format, chain GA [auth H] mmCIF format, chain CA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth F]	AA [auth F] BA [auth F] CA [auth F] EA [auth G] FA [auth G] AA [auth F], BA [auth F], CA [auth F], EA [auth G], FA [auth G], GA [auth H], HA [auth H], IA [auth I], JA [auth I], KA [auth I], LA [auth J], M [auth A], MA [auth J], N [auth A], NA [auth K], O [auth A], OA [auth K], P [auth B], PA [auth L], Q [auth B], QA [auth L], R [auth C], S [auth C], T [auth C], U [auth D], V [auth D], W [auth D], X [auth E], Y [auth E], Z [auth E]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain LA [auth J] Focus chain M [auth A] Focus chain MA [auth J] Focus chain N [auth A] Focus chain NA [auth K] Focus chain O [auth A] Focus chain OA [auth K] Focus chain P [auth B] Focus chain PA [auth L] Focus chain Q [auth B] Focus chain QA [auth L] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain GA [auth H] Focus chain HA [auth H] Focus chain IA [auth I] Focus chain JA [auth I] Focus chain KA [auth I] Focus chain LA [auth J] Focus chain M [auth A] Focus chain MA [auth J] Focus chain N [auth A] Focus chain NA [auth K] Focus chain O [auth A] Focus chain OA [auth K] Focus chain P [auth B] Focus chain PA [auth L] Focus chain Q [auth B] Focus chain QA [auth L] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.267 (Depositor), 0.267 (DCC)
R-Value Work: 0.224 (Depositor), 0.225 (DCC)
R-Value Observed: 0.224 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 111	α = 112.3
b = 111	β = 101.6
c = 112.4	γ = 114.3

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASES	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2015-06-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-06-10
Type: Initial release
Version 1.1: 2015-06-24
Changes: Non-polymer description
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description