5HE8 | pdb_00005he8

Bacterial initiation protein

PDB DOI: https://doi.org/10.2210/pdb5HE8/pdb

Classification: PROTEIN BINDING
Organism(s): Staphylococcus aureus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-01-05 Released: 2016-06-08
Deposition Author(s): Hood, I.V., Berger, J.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Department of Energy (DOE, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free:
0.270 (Depositor), 0.270 (DCC)
R-Value Work:
0.225 (Depositor), 0.230 (DCC)
R-Value Observed:
0.227 (Depositor)

wwPDB Validation 3D Report Full Report

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

Literature

Bacterial initiation protein

Hood, I.V., Berger, J.M.

To be published.

Macromolecule Content

Total Structure Weight: 239.1 kDa
Atom Count: 16,104
Modeled Residue Count: 1,982
Deposited Residue Count: 2,088
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Helicase loader	A B C D E A, B, C, D, E, F, G, H, I, J, K [auth L], L [auth K]	174	Staphylococcus aureus	Mutation(s): 0 Gene Names: dnaI
UniProt
Find proteins for Q2FXP5 (Staphylococcus aureus (strain NCTC 8325 / PS 47)) Explore Q2FXP5 Go to UniProtKB: Q2FXP5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2FXP5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain AA [auth G] SDF format, chain BA [auth G] SDF format, chain CA [auth H] SDF format, chain DA [auth H] SDF format, chain EA [auth H] SDF format, chain FA [auth H] SDF format, chain GA [auth I] SDF format, chain HA [auth I] SDF format, chain IA [auth J] SDF format, chain JA [auth J] SDF format, chain KA [auth L] SDF format, chain LA [auth L] SDF format, chain M [auth A] SDF format, chain MA [auth K] SDF format, chain N [auth A] SDF format, chain NA [auth K] SDF format, chain O [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain W [auth E] SDF format, chain Y [auth F] SDF format, chain Z [auth F] SDF format, chain X [auth E] MOL2 format, chain AA [auth G] MOL2 format, chain BA [auth G] MOL2 format, chain CA [auth H] MOL2 format, chain DA [auth H] MOL2 format, chain EA [auth H] MOL2 format, chain FA [auth H] MOL2 format, chain GA [auth I] MOL2 format, chain HA [auth I] MOL2 format, chain IA [auth J] MOL2 format, chain JA [auth J] MOL2 format, chain KA [auth L] MOL2 format, chain LA [auth L] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth K] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth K] MOL2 format, chain O [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain W [auth E] MOL2 format, chain Y [auth F] MOL2 format, chain Z [auth F] MOL2 format, chain X [auth E] mmCIF format, chain AA [auth G] mmCIF format, chain BA [auth G] mmCIF format, chain CA [auth H] mmCIF format, chain DA [auth H] mmCIF format, chain EA [auth H] mmCIF format, chain FA [auth H] mmCIF format, chain GA [auth I] mmCIF format, chain HA [auth I] mmCIF format, chain IA [auth J] mmCIF format, chain JA [auth J] mmCIF format, chain KA [auth L] mmCIF format, chain LA [auth L] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth K] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth K] mmCIF format, chain O [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain W [auth E] mmCIF format, chain Y [auth F] mmCIF format, chain Z [auth F] mmCIF format, chain X [auth E]	AA [auth G] BA [auth G] CA [auth H] DA [auth H] EA [auth H] AA [auth G], BA [auth G], CA [auth H], DA [auth H], EA [auth H], FA [auth H], GA [auth I], HA [auth I], IA [auth J], JA [auth J], KA [auth L], LA [auth L], M [auth A], MA [auth K], N [auth A], NA [auth K], O [auth A], P [auth B], Q [auth C], R [auth C], S [auth C], T [auth C], U [auth D], V [auth D], W [auth E], X [auth E], Y [auth F], Z [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain IA [auth J] Focus chain JA [auth J] Focus chain KA [auth L] Focus chain LA [auth L] Focus chain M [auth A] Focus chain MA [auth K] Focus chain N [auth A] Focus chain NA [auth K] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] 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 E] Focus chain X [auth E] Focus chain Y [auth F] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth G] Focus chain BA [auth G] Focus chain CA [auth H] Focus chain DA [auth H] Focus chain EA [auth H] Focus chain FA [auth H] Focus chain GA [auth I] Focus chain HA [auth I] Focus chain IA [auth J] Focus chain JA [auth J] Focus chain KA [auth L] Focus chain LA [auth L] Focus chain M [auth A] Focus chain MA [auth K] Focus chain N [auth A] Focus chain NA [auth K] Focus chain O [auth A] Focus chain P [auth B] Focus chain Q [auth C] 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 E] Focus chain X [auth E] Focus chain Y [auth F] Focus chain Z [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.60 Å
R-Value Free: 0.270 (Depositor), 0.270 (DCC)
R-Value Work: 0.225 (Depositor), 0.230 (DCC)
R-Value Observed: 0.227 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.099	α = 90
b = 126.261	β = 90
c = 183.344	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2016-06-08

Deposition Author(s):

Hood, I.V.

Berger, J.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM071747
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32 GM 007232
Department of Energy (DOE, United States)	United States	Department of Energy Office of Science Graduate Fellowship

Revision History (Full details and data files)

Version 1.0: 2016-06-08
Type: Initial release
Version 1.1: 2017-09-20
Changes: Author supporting evidence, Derived calculations
Version 1.2: 2019-12-04
Changes: Author supporting evidence
Version 1.3: 2024-11-06
Changes: Data collection, Database references, Structure summary