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- PDB-6b7j: The crystal structure of 3-hydroxydecanoyl-(acyl carrier protein)... -

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Basic information

Entry
Database: PDB / ID: 6b7j
TitleThe crystal structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Vibrio cholerae O1 biovar eltor str. N16961
Components3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
KeywordsLYASE / structural genomics / The 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 / (3R)-3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity / (3R)-3-hydroxymyristoyl-[acyl-carrier-protein] dehydratase activity / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / fatty acid biosynthetic process / 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
FORMIC ACID / 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsTan, K. / Gu, M. / Nocek, B. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: The crystal structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Vibrio cholerae O1 biovar eltor str. N16961
Authors: Tan, K. / Gu, M. / Nocek, B. / Joachimiak, A.
History
DepositionOct 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 23, 2022Group: Advisory / Author supporting evidence / Database references
Category: database_2 / pdbx_audit_support / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7634
Polymers38,6712
Non-polymers922
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-18 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.520, 85.263, 49.932
Angle α, β, γ (deg.)90.00, 97.11, 90.00
Int Tables number4
Space group name H-MP1211

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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: 19335.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: fabA, VC0395_A1091, VC395_1603 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic
References: UniProt: A5F850, 3-hydroxyacyl-[acyl-carrier-protein] dehydratase, trans-2-decenoyl-[acyl-carrier protein] isomerase
#2: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.005 M CaCl2, 0.1 < Bis-Tris, 30% v/v PEG MME 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.44→26.25 Å / Num. obs: 59933 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 12.67 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.032 / Rrim(I) all: 0.061 / Χ2: 1.883 / Net I/σ(I): 36.87
Reflection shellResolution: 1.44→1.48 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 5.58 / Num. unique obs: 2995 / CC1/2: 0.937 / Rpim(I) all: 0.197 / Rrim(I) all: 0.381 / Χ2: 1.454 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MKB

1mkb


Resolution: 1.44→26.25 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.86
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 2937 4.9 %random
Rwork0.1559 ---
obs0.1578 59896 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.44→26.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2667 0 6 326 2999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062829
X-RAY DIFFRACTIONf_angle_d0.8533828
X-RAY DIFFRACTIONf_dihedral_angle_d7.4721977
X-RAY DIFFRACTIONf_chiral_restr0.083410
X-RAY DIFFRACTIONf_plane_restr0.005502
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4423-1.46590.32551120.22962279X-RAY DIFFRACTION84
1.4659-1.49120.28041390.19942760X-RAY DIFFRACTION100
1.4912-1.51830.24851380.19382733X-RAY DIFFRACTION100
1.5183-1.54750.22451440.17862752X-RAY DIFFRACTION100
1.5475-1.57910.22091470.17442698X-RAY DIFFRACTION100
1.5791-1.61340.21291280.17272755X-RAY DIFFRACTION100
1.6134-1.65090.22761400.16582710X-RAY DIFFRACTION100
1.6509-1.69220.19861490.16142741X-RAY DIFFRACTION100
1.6922-1.7380.18971330.15372732X-RAY DIFFRACTION100
1.738-1.78910.20231460.16262739X-RAY DIFFRACTION100
1.7891-1.84680.2081220.16562767X-RAY DIFFRACTION100
1.8468-1.91280.18811640.16262676X-RAY DIFFRACTION100
1.9128-1.98940.22161150.16062774X-RAY DIFFRACTION100
1.9894-2.07990.19891320.16272746X-RAY DIFFRACTION100
2.0799-2.18950.18171520.16382724X-RAY DIFFRACTION100
2.1895-2.32660.2051450.16582714X-RAY DIFFRACTION100
2.3266-2.50610.18541630.16082745X-RAY DIFFRACTION100
2.5061-2.7580.1811490.16952725X-RAY DIFFRACTION100
2.758-3.15660.22131410.16092767X-RAY DIFFRACTION100
3.1566-3.97470.18541450.13872692X-RAY DIFFRACTION98
3.9747-26.24930.15651330.12512730X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.96110.98431.56486.73011.43096.1004-0.0401-0.8994-0.06151.01380.147-0.4742-0.02330.3260.01820.37450.0015-0.02570.30430.00070.280514.8303-5.974116.9863
24.2055-1.5392-0.69786.2427-1.09564.0237-0.1732-0.49750.02710.5770.1080.10860.00320.0611-0.03950.22550.04330.03860.19750.02170.1438.55060.973116.1693
33.5229-0.65410.70094.7452-0.6013.37950.05930.0037-0.0585-0.14020.06590.13260.0015-0.1363-0.11950.13980.00060.04010.12-0.00230.17814.96252.35645.6862
44.1467-0.2045-0.54521.7891-0.64251.0875-0.1987-0.2532-0.2281-0.0990.0276-0.21240.14370.20610.01480.16570.0030.00480.14960.01210.273421.1037-7.473.845
51.564-0.43910.87980.9991-0.5781.08220.0078-0.0071-0.0673-0.01050.04130.0570.0104-0.0155-0.06510.13010.00070.02370.1152-0.00130.19675.52421.28-1.8091
61.6086-0.11390.7641.6044-0.28661.5883-0.03930.0182-0.0172-0.02850.0352-0.0414-0.06370.01360.04820.10810.01390.03480.0658-0.00390.180511.65543.4962-2.9154
74.47090.10481.11741.9671-0.33712.068-0.1691-0.120.0692-0.06360.0571-0.1923-0.05860.18450.03940.12470.00590.01660.134-0.0120.218419.5389-2.0079-0.3502
84.99080.41550.21144.63241.49743.8327-0.0092-0.03190.08350.21770.3751-0.596-0.16880.6523-0.32680.14810.00610.02160.1452-0.00750.274321.28153.11020.9393
94.70261.9410.3077.77752.125.0276-0.17270.4742-0.4229-0.34460.1826-0.19730.03870.1413-0.05080.12910.0220.02960.1166-0.03290.191812.9351-2.8717-10.7039
103.8369-0.67830.11747.17263.19075.0423-0.0286-0.44890.52690.47040.0885-0.2779-0.47930.1516-0.1720.2524-0.0138-0.01260.1499-0.03830.31818.971613.7077.8399
114.079-0.33490.14496.1943-1.73123.8033-0.06040.42480.2345-0.44560.12770.3385-0.1072-0.2193-0.06630.1406-0.0038-0.00680.16530.040.2158-6.091319.0811-15.0873
120.9119-0.30090.16411.476-0.10231.89080.00340.14040.0897-0.10890.0104-0.0801-0.02910.0045-0.01370.1278-0.00650.04550.11370.00620.18647.522717.9092-10.3783
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 9 )
2X-RAY DIFFRACTION2chain 'A' and (resid 10 through 27 )
3X-RAY DIFFRACTION3chain 'A' and (resid 28 through 38 )
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 53 )
5X-RAY DIFFRACTION5chain 'A' and (resid 54 through 97 )
6X-RAY DIFFRACTION6chain 'A' and (resid 98 through 123 )
7X-RAY DIFFRACTION7chain 'A' and (resid 124 through 135 )
8X-RAY DIFFRACTION8chain 'A' and (resid 136 through 150 )
9X-RAY DIFFRACTION9chain 'A' and (resid 151 through 159 )
10X-RAY DIFFRACTION10chain 'A' and (resid 160 through 172 )
11X-RAY DIFFRACTION11chain 'B' and (resid 0 through 38 )
12X-RAY DIFFRACTION12chain 'B' and (resid 39 through 172 )

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