3TYH | pdb_00003tyh

Crystal structure of oxo-cupper clusters binding to ferric binding protein from Neisseria gonorrhoeae

PDB DOI: https://doi.org/10.2210/pdb3TYH/pdb

Classification: METAL TRANSPORT
Organism(s): Neisseria gonorrhoeae
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2011-09-26 Released: 2012-09-26
Deposition Author(s): Chen, W.J., Wang, H.F., Zhou, C.J., Ye, D.R., Huang, J., Tan, X.S., Zhong, W.Q.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.169 (Depositor), 0.168 (DCC)
R-Value Work:
0.143 (Depositor), 0.146 (DCC)
R-Value Observed:
0.144 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of oxo-cupper clusters binding to ferric binding protein from Neisseria gonorrhoeae

Chen, W.J., Wang, H.F., Zhou, C.J., Ye, D.R., Huang, J., Tan, X.S., Zhong, W.Q.

To be published.

Macromolecule Content

Total Structure Weight: 304.34 kDa
Atom Count: 22,889
Modeled Residue Count: 2,781
Deposited Residue Count: 2,781
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FbpA protein	A, B, C, D, E A, B, C, D, E, F, G, H, I	309	Neisseria gonorrhoeae	Mutation(s): 0 Gene Names: FbpA
UniProt
Find proteins for P17259 (Neisseria gonorrhoeae) Explore P17259 Go to UniProtKB: P17259
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P17259
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU Query on CU Download:Ideal Coordinates CCD File SDF format, chain Z [auth I] SDF format, chain Y [auth H] SDF format, chain X [auth H] SDF format, chain W [auth G] SDF format, chain V [auth G] SDF format, chain U [auth F] SDF format, chain T [auth F] SDF format, chain S [auth E] SDF format, chain R [auth E] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain M [auth B] SDF format, chain L [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain AA [auth I] MOL2 format, chain Z [auth I] MOL2 format, chain Y [auth H] MOL2 format, chain X [auth H] MOL2 format, chain W [auth G] MOL2 format, chain V [auth G] MOL2 format, chain U [auth F] MOL2 format, chain T [auth F] MOL2 format, chain S [auth E] MOL2 format, chain R [auth E] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain M [auth B] MOL2 format, chain L [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain AA [auth I] mmCIF format, chain Z [auth I] mmCIF format, chain Y [auth H] mmCIF format, chain X [auth H] mmCIF format, chain W [auth G] mmCIF format, chain V [auth G] mmCIF format, chain U [auth F] mmCIF format, chain T [auth F] mmCIF format, chain S [auth E] mmCIF format, chain R [auth E] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain M [auth B] mmCIF format, chain L [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain AA [auth I]	AA [auth I] J [auth A] K [auth A] L [auth B] M [auth B] AA [auth I], J [auth A], K [auth A], L [auth B], M [auth B], N [auth C], O [auth C], P [auth D], Q [auth D], R [auth E], S [auth E], T [auth F], U [auth F], V [auth G], W [auth G], X [auth H], Y [auth H], Z [auth I]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth H] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth I] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain T [auth F] Focus chain U [auth F] Focus chain V [auth G] Focus chain W [auth G] Focus chain X [auth H] Focus chain Y [auth H] Focus chain Z [auth I]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.169 (Depositor), 0.168 (DCC)
R-Value Work: 0.143 (Depositor), 0.146 (DCC)
R-Value Observed: 0.144 (Depositor)

Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 146.514	α = 90
b = 146.514	β = 90
c = 114.59	γ = 120

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2012-09-26

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2012-09-26
Type: Initial release
Version 1.1: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description