5HD6

High resolution structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Yersinia pestis at 1.35 A

PDB DOI: https://doi.org/10.2210/pdb5HD6/pdb

Classification: LYASE
Organism(s): Yersinia pestis CO92
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-01-04 Released: 2016-01-20
Deposition Author(s): Chang, C., Maltseva, N., Kim, Y., Mulligan, R., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.170
R-Value Work: 0.136
R-Value Observed: 0.138

wwPDB Validation 3D Report Full Report

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

Literature

High resolution structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Yersinia pestis at 1.35 A

Chang, C., Maltseva, N., Kim, Y., Mulligan, R., Kwon, K., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 157.59 kDa
Atom Count: 12,776
Modelled Residue Count: 1,381
Deposited Residue Count: 1,400
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase	A, B, C, D, E A, B, C, D, E, F, G, H	175	Yersinia pestis CO92	Mutation(s): 0 Gene Names: fabA, AK38_1122 EC: 4.2.1.59
UniProt
Find proteins for Q8ZG80 (Yersinia pestis) Explore Q8ZG80 Go to UniProtKB: Q8ZG80
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8ZG80
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth B] SDF format, chain K [auth C] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain N [auth D] SDF format, chain O [auth D] SDF format, chain P [auth E] SDF format, chain Q [auth F] SDF format, chain R [auth F] SDF format, chain S [auth G] SDF format, chain T [auth G] SDF format, chain U [auth H] SDF format, chain V [auth H] SDF format, chain W [auth H] MOL2 format, chain I [auth A] MOL2 format, chain J [auth B] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain N [auth D] MOL2 format, chain O [auth D] MOL2 format, chain P [auth E] MOL2 format, chain Q [auth F] MOL2 format, chain R [auth F] MOL2 format, chain S [auth G] MOL2 format, chain T [auth G] MOL2 format, chain U [auth H] MOL2 format, chain V [auth H] MOL2 format, chain W [auth H]	I [auth A] J [auth B] K [auth C] L [auth C] M [auth C] I [auth A], J [auth B], K [auth C], L [auth C], M [auth C], N [auth D], O [auth D], P [auth E], Q [auth F], R [auth F], S [auth G], T [auth G], U [auth H], V [auth H], W [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth D] Focus chain P [auth E] Focus chain Q [auth F] Focus chain R [auth F] Focus chain S [auth G] Focus chain T [auth G] Focus chain U [auth H] Focus chain V [auth H] Focus chain W [auth H]

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	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.35 Å
R-Value Free: 0.170
R-Value Work: 0.136
R-Value Observed: 0.138
Space Group: P 1
Diffraction Data: https://doi.org/10.18430/M35HD6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.665	α = 90.02
b = 50.816	β = 90.02
c = 138.78	γ = 90.1

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-3000	data reduction
MOLREP	phasing
SBC-Collect	data collection
Coot	model building

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2016-01-20

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2016-01-20
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.2: 2023-11-15
Changes: Data collection

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Deposit Data

Help and Resources

5HD6

High resolution structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Yersinia pestis at 1.35 A

High resolution structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Yersinia pestis at 1.35 A

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)