3GSD

2.05 Angstrom structure of a divalent-cation tolerance protein (CutA) from Yersinia pestis

PDB DOI: https://doi.org/10.2210/pdb3GSD/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Yersinia pestis CO92
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-03-26 Released: 2009-04-07
Deposition Author(s): Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.200
R-Value Work: 0.156
R-Value Observed: 0.159

wwPDB Validation 3D Report Full Report

This is version 1.4 of the entry. See complete history.

Literature

2.05 Angstrom Structure of a Divalent-cation Tolerance Protein (CutA) from Yersinia pestis

Minasov, G., Wawrzak, Z., Skarina, T., Onopriyenko, O., Peterson, S.N., Savchenko, A., Anderson, W.F.

To be published.

Macromolecule Content

Total Structure Weight: 167.64 kDa
Atom Count: 12,069
Modelled Residue Count: 1,258
Deposited Residue Count: 1,464
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Divalent-cation tolerance protein cutA	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	122	Yersinia pestis CO92	Mutation(s): 0 Gene Names: cutA, y0604, YPO0346, YP_0500
UniProt
Find proteins for Q74XD3 (Yersinia pestis) Explore Q74XD3 Go to UniProtKB: Q74XD3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q74XD3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download Ideal Coordinates CCD File SDF format, chain AB [auth J] SDF format, chain CA [auth D] SDF format, chain DB [auth K] SDF format, chain FA [auth E] SDF format, chain IB [auth L] SDF format, chain JB [auth L] SDF format, chain LA [auth F] SDF format, chain PA [auth G] SDF format, chain Q [auth A] SDF format, chain SA [auth H] SDF format, chain U [auth B] SDF format, chain XA [auth I] SDF format, chain Y [auth C] MOL2 format, chain AB [auth J] MOL2 format, chain CA [auth D] MOL2 format, chain DB [auth K] MOL2 format, chain FA [auth E] MOL2 format, chain IB [auth L] MOL2 format, chain JB [auth L] MOL2 format, chain LA [auth F] MOL2 format, chain PA [auth G] MOL2 format, chain Q [auth A] MOL2 format, chain SA [auth H] MOL2 format, chain U [auth B] MOL2 format, chain XA [auth I] MOL2 format, chain Y [auth C]	AB [auth J] CA [auth D] DB [auth K] FA [auth E] IB [auth L] AB [auth J], CA [auth D], DB [auth K], FA [auth E], IB [auth L], JB [auth L], LA [auth F], PA [auth G], Q [auth A], SA [auth H], U [auth B], XA [auth I], Y [auth C]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain AB [auth J] Focus chain CA [auth D] Focus chain DB [auth K] Focus chain FA [auth E] Focus chain IB [auth L] Focus chain JB [auth L] Focus chain LA [auth F] Focus chain PA [auth G] Focus chain Q [auth A] Focus chain SA [auth H] Focus chain U [auth B] Focus chain XA [auth I] Focus chain Y [auth C] Interactions & Density Focus chain AB [auth J] Focus chain CA [auth D] Focus chain DB [auth K] Focus chain FA [auth E] Focus chain IB [auth L] Focus chain JB [auth L] Focus chain LA [auth F] Focus chain PA [auth G] Focus chain Q [auth A] Focus chain SA [auth H] Focus chain U [auth B] Focus chain XA [auth I] Focus chain Y [auth C]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CB [auth K] SDF format, chain EA [auth E] SDF format, chain HB [auth L] SDF format, chain JA [auth F] SDF format, chain OA [auth G] SDF format, chain P [auth A] SDF format, chain QA [auth H] SDF format, chain T [auth B] SDF format, chain W [auth C] SDF format, chain WA [auth I] SDF format, chain ZA [auth J] MOL2 format, chain BA [auth D] MOL2 format, chain CB [auth K] MOL2 format, chain EA [auth E] MOL2 format, chain HB [auth L] MOL2 format, chain JA [auth F] MOL2 format, chain OA [auth G] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth H] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] MOL2 format, chain WA [auth I] MOL2 format, chain ZA [auth J]	BA [auth D] CB [auth K] EA [auth E] HB [auth L] JA [auth F] BA [auth D], CB [auth K], EA [auth E], HB [auth L], JA [auth F], OA [auth G], P [auth A], QA [auth H], T [auth B], W [auth C], WA [auth I], ZA [auth J]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CB [auth K] Focus chain EA [auth E] Focus chain HB [auth L] Focus chain JA [auth F] Focus chain OA [auth G] Focus chain P [auth A] Focus chain QA [auth H] Focus chain T [auth B] Focus chain W [auth C] Focus chain WA [auth I] Focus chain ZA [auth J] Interactions & Density Focus chain BA [auth D] Focus chain CB [auth K] Focus chain EA [auth E] Focus chain HB [auth L] Focus chain JA [auth F] Focus chain OA [auth G] Focus chain P [auth A] Focus chain QA [auth H] Focus chain T [auth B] Focus chain W [auth C] Focus chain WA [auth I] Focus chain ZA [auth J]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain KA [auth F] SDF format, chain RA [auth H] SDF format, chain X [auth C] MOL2 format, chain KA [auth F] MOL2 format, chain RA [auth H] MOL2 format, chain X [auth C]	KA [auth F], RA [auth H], X [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain KA [auth F] Focus chain RA [auth H] Focus chain X [auth C] Interactions & Density Focus chain KA [auth F] Focus chain RA [auth H] Focus chain X [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain EB [auth L] SDF format, chain AA [auth D] SDF format, chain BB [auth K] SDF format, chain DA [auth E] SDF format, chain FB [auth L] SDF format, chain GA [auth F] SDF format, chain GB [auth L] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain M [auth A] SDF format, chain MA [auth G] SDF format, chain N [auth A] SDF format, chain NA [auth G] SDF format, chain O [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain TA [auth I] SDF format, chain UA [auth I] SDF format, chain V [auth C] SDF format, chain VA [auth I] SDF format, chain YA [auth J] SDF format, chain Z [auth D] MOL2 format, chain EB [auth L] MOL2 format, chain AA [auth D] MOL2 format, chain BB [auth K] MOL2 format, chain DA [auth E] MOL2 format, chain FB [auth L] MOL2 format, chain GA [auth F] MOL2 format, chain GB [auth L] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth G] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth G] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain TA [auth I] MOL2 format, chain UA [auth I] MOL2 format, chain V [auth C] MOL2 format, chain VA [auth I] MOL2 format, chain YA [auth J] MOL2 format, chain Z [auth D]	AA [auth D] BB [auth K] DA [auth E] EB [auth L] FB [auth L] AA [auth D], BB [auth K], DA [auth E], EB [auth L], FB [auth L], GA [auth F], GB [auth L], HA [auth F], IA [auth F], M [auth A], MA [auth G], N [auth A], NA [auth G], O [auth A], R [auth B], S [auth B], TA [auth I], UA [auth I], V [auth C], VA [auth I], YA [auth J], Z [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain BB [auth K] Focus chain DA [auth E] Focus chain EB [auth L] Focus chain FB [auth L] Focus chain GA [auth F] Focus chain GB [auth L] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain NA [auth G] Focus chain O [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain TA [auth I] Focus chain UA [auth I] Focus chain V [auth C] Focus chain VA [auth I] Focus chain YA [auth J] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BB [auth K] Focus chain DA [auth E] Focus chain EB [auth L] Focus chain FB [auth L] Focus chain GA [auth F] Focus chain GB [auth L] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain M [auth A] Focus chain MA [auth G] Focus chain N [auth A] Focus chain NA [auth G] Focus chain O [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain TA [auth I] Focus chain UA [auth I] Focus chain V [auth C] Focus chain VA [auth I] Focus chain YA [auth J] Focus chain Z [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.05 Å
R-Value Free: 0.200
R-Value Work: 0.156
R-Value Observed: 0.159
Space Group: C 2 2 2₁
Diffraction Data: https://doi.org/10.18430/M33GSD

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.782	α = 90
b = 157.914	β = 90
c = 157.132	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
BALBES	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2009-04-07

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2009-04-07
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-11-01
Changes: Refinement description
Version 1.3: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.4: 2023-11-22
Changes: Data collection