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- PDB-5hd6: High resolution structure of 3-hydroxydecanoyl-(acyl carrier prot... -

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Basic information

Entry
Database: PDB / ID: 5hd6
TitleHigh resolution structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Yersinia pestis at 1.35 A
Components3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
KeywordsLYASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


trans-2-decenoyl-[acyl-carrier protein] isomerase / trans-2-decenoyl-acyl-carrier-protein isomerase activity / unsaturated fatty acid biosynthetic process / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity / cytoplasm
Similarity search - Function
Beta-hydroxyacyl-(acyl-carrier-protein) dehydratase FabA / Beta-hydroxydecanoyl thiol ester dehydrase, FabA/FabZ / FabA-like domain / Hotdog Thioesterase / Thiol Ester Dehydrase; Chain A / HotDog domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
: / 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsChang, C. / Maltseva, N. / Kim, Y. / Mulligan, R. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: High resolution structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Yersinia pestis at 1.35 A
Authors: Chang, C. / Maltseva, N. / Kim, Y. / Mulligan, R. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 4, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
B: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
C: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
D: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
E: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
F: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
G: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
H: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)157,59123
Polymers156,2098
Non-polymers1,38115
Water29,4371634
1
A: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
G: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3295
Polymers39,0522
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-25 kcal/mol
Surface area13370 Å2
MethodPISA
2
B: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
F: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3295
Polymers39,0522
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4140 Å2
ΔGint-25 kcal/mol
Surface area13480 Å2
MethodPISA
3
C: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
E: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4216
Polymers39,0522
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-25 kcal/mol
Surface area13720 Å2
MethodPISA
4
D: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
H: 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5137
Polymers39,0522
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-25 kcal/mol
Surface area13810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.665, 50.816, 138.780
Angle α, β, γ (deg.)90.020, 90.020, 90.100
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabA / Beta-hydroxydecanoyl thioester dehydrase / ...3-hydroxyacyl-[acyl-carrier-protein] dehydratase FabA / Beta-hydroxydecanoyl thioester dehydrase / Trans-2-decenoyl-[acyl-carrier-protein] isomerase


Mass: 19526.186 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: fabA, AK38_1122 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0B6NZG1, UniProt: Q8ZG80*PLUS, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1634 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.52 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.16 M magnesium chloride, 0.08 M Tris-HCl, 24 % PEG 4000, 20 % glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97921 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 3, 2014
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 241931 / % possible obs: 94.6 % / Redundancy: 2.2 % / Biso Wilson estimate: 9.72 Å2 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.038 / Rrim(I) all: 0.057 / Χ2: 0.917 / Net I/av σ(I): 17.972 / Net I/σ(I): 10.6 / Num. measured all: 521903
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.35-1.371.90.21997160.880.2010.2980.69775.2
1.37-1.41.90.201115920.8960.1850.2740.7591.8
1.4-1.432.10.196119310.9020.180.2670.77493.3
1.43-1.452.20.172120420.9230.1570.2340.80994
1.45-1.492.20.148120580.9430.1350.2010.82494.2
1.49-1.522.20.126120770.9550.1150.1710.88394.5
1.52-1.562.20.11120310.9670.10.1490.89594.7
1.56-1.62.20.101122140.970.0920.1370.90795
1.6-1.652.20.093122000.9750.0840.1260.90895.2
1.65-1.72.20.079122690.980.0720.1070.93895.5
1.7-1.762.20.069121350.9850.0630.0940.96995.6
1.76-1.832.20.061123090.9870.0560.0830.9796.1
1.83-1.922.20.053122230.990.0480.0720.98696.2
1.92-2.022.20.047123930.9920.0420.0630.99196.5
2.02-2.142.20.043124230.9930.0390.0581.01397
2.14-2.312.20.041124050.9930.0370.0561.0797.1
2.31-2.542.20.042124490.9920.0380.0571.17397.3
2.54-2.912.20.038124640.9940.0340.0511.11497.8
2.91-3.662.10.029125600.9970.0260.0390.90298.3
3.66-502.20.023124400.9970.0210.0310.62297.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
MOLREPphasing
SBC-Collectdata collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q62

3q62


Resolution: 1.35→26.915 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 16.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1703 21576 4.88 %
Rwork0.1362 420193 -
obs0.1378 241904 86.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.41 Å2 / Biso mean: 14.704 Å2 / Biso min: 4.3 Å2
Refinement stepCycle: final / Resolution: 1.35→26.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10576 0 96 1634 12306
Biso mean--30.03 28.11 -
Num. residues----1380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00711401
X-RAY DIFFRACTIONf_angle_d0.87715370
X-RAY DIFFRACTIONf_chiral_restr0.0841600
X-RAY DIFFRACTIONf_plane_restr0.0052006
X-RAY DIFFRACTIONf_dihedral_angle_d19.6194266
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3501-1.36550.25814730.20088959943255
1.3655-1.38150.25075120.1867109431145567
1.3815-1.39840.23676460.1798117931243974
1.3984-1.41610.23376610.1703128051346678
1.4161-1.43470.21246470.1644136171426484
1.4347-1.45430.21147560.1618137461450285
1.4543-1.47510.2216140.1539139411455585
1.4751-1.49710.20676350.1459138841451985
1.4971-1.52050.18117410.137138101455186
1.5205-1.54550.18456870.1322139811466886
1.5455-1.57210.17386260.1254142161484286
1.5721-1.60070.17658390.1324138731471287
1.6007-1.63150.17887930.1353141401493387
1.6315-1.66480.18828020.1302139231472587
1.6648-1.7010.17157490.1214145121526188
1.701-1.74050.17548870.1201139841487188
1.7405-1.7840.16317520.1198143041505688
1.784-1.83230.16986950.1262145691526489
1.8323-1.88620.14687020.1177144581516089
1.8862-1.9470.15667970.118146921548990
1.947-2.01660.16327310.1241145741530590
2.0166-2.09730.1577280.125146061533491
2.0973-2.19270.15057730.1217148561562991
2.1927-2.30830.16048710.1241148751574692
2.3083-2.45280.16227200.1356149391565992
2.4528-2.6420.17437410.1535150791582093
2.642-2.90760.20038180.1554150951591393
2.9076-3.32770.17077720.1416151271589993
3.3277-4.190.14346830.1238154901617395
4.19-26.920.15097250.1482154021612794

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