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- PDB-4wjz: Crystal structure of beta-ketoacyl-acyl carrier protein reductase... -

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Basic information

Entry
Database: PDB / ID: 4wjz
TitleCrystal structure of beta-ketoacyl-acyl carrier protein reductase (FabG)(G141A) from Vibrio cholerae
Components3-oxoacyl-[acyl-carrier-protein] reductase FabG
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / Vibrio cholerae / FabG / beta-ketoacyl-acyl carrier protein reductase
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsHou, J. / Zheng, H. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: J.Bacteriol. / Year: 2015
Title: Dissecting the Structural Elements for the Activation of beta-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae.
Authors: Hou, J. / Zheng, H. / Chruszcz, M. / Zimmerman, M.D. / Shumilin, I.A. / Osinski, T. / Demas, M. / Grimshaw, S. / Minor, W.
History
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Data collection
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Feb 3, 2016Group: Database references
Revision 1.4Sep 27, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.6Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.7Dec 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
C: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
D: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,6796
Polymers105,4894
Non-polymers1902
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-53 kcal/mol
Surface area36570 Å2
Unit cell
Length a, b, c (Å)61.825, 61.825, 384.704
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA2 - 2465 - 249
21SERSERBB2 - 2465 - 249
12ALAALAAA0 - 2463 - 249
22ALAALACC0 - 2463 - 249
13METMETAA1 - 2464 - 249
23METMETDD1 - 2464 - 249
14SERSERBB2 - 2465 - 249
24SERSERCC2 - 2465 - 249
15SERSERBB2 - 2465 - 249
25SERSERDD2 - 2465 - 249
16METMETCC1 - 2464 - 249
26METMETDD1 - 2464 - 249

NCS ensembles :
ID
1
2
3
4
5
6
DetailsThe biological assembly is a tetramer.

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Components

#1: Protein
3-oxoacyl-[acyl-carrier-protein] reductase FabG / 3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta- ...3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta-ketoacyl-ACP reductase


Mass: 26372.141 Da / Num. of mol.: 4 / Mutation: G141A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Gene: fabG, VC_2021 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q9KQH7, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.01 Å3/Da / Density % sol: 38.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 2.4M Ammonium phosphate, 0.1M Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 25, 2014 / Details: Beyllium Lenses
RadiationMonochromator: Diamond 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionRedundancy: 5.8 % / Number: 185974 / Rmerge(I) obs: 0.091 / Χ2: 0.88 / D res high: 2.4 Å / D res low: 27 Å / Num. obs: 32068 / % possible obs: 98.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
6.492710.0340.6064.3
5.166.4910.0510.85.9
4.515.1610.0541.0135.5
4.14.5110.0550.9785.5
3.814.110.060.9495.9
3.583.8110.0681.0216
3.43.5810.0791.0926.1
3.263.410.0950.9296.2
3.133.2610.1240.8896.4
3.023.1310.1470.8546.3
2.933.0210.1630.8496.3
2.852.9310.2010.8446.3
2.772.8510.240.8066.3
2.72.7710.2660.8126.3
2.642.710.3530.8786.3
2.592.6410.3860.8356.2
2.532.5910.470.8335.7
2.492.5310.4850.7935.2
2.442.4910.5180.7924.8
2.42.4410.5650.8334.1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.758
11K, H, -L20.242
ReflectionResolution: 2.4→27 Å / Num. obs: 32068 / % possible obs: 98.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.041 / Rrim(I) all: 0.1 / Χ2: 0.877 / Net I/av σ(I): 17.676 / Net I/σ(I): 8.1 / Num. measured all: 185974
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.4-2.444.10.56515530.6040.3070.6470.83397.2
2.44-2.494.80.51816280.7160.2620.5830.79297.7
2.49-2.535.20.48515740.7760.2320.5390.79399.1
2.53-2.595.70.4716410.8010.2150.5180.83399.8
2.59-2.646.20.38616050.8750.1660.4210.83599.9
2.64-2.76.30.35316430.8740.1520.3840.878100
2.7-2.776.30.26615740.9240.1140.290.81299.9
2.77-2.856.30.2416370.9370.1030.2620.806100
2.85-2.936.30.20116440.9540.0860.2190.844100
2.93-3.026.30.16315890.9720.070.1770.849100
3.02-3.136.30.14716280.9760.0630.160.85499.8
3.13-3.266.40.12416500.980.0530.1350.88999.8
3.26-3.46.20.09515890.9870.0410.1030.92999.9
3.4-3.586.10.07916300.9880.0340.0871.09299.4
3.58-3.8160.06816120.990.030.0741.02199.3
3.81-4.15.90.0616140.9920.0270.0660.94998.4
4.1-4.515.50.05515850.990.0250.0610.97898.7
4.51-5.165.50.05416190.9910.0240.0591.01397.8
5.16-6.495.90.05115800.9910.0230.0560.898.6
6.49-274.30.03414730.9930.0180.0380.60687.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data reduction
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→26.94 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.886 / WRfactor Rfree: 0.2295 / WRfactor Rwork: 0.1946 / FOM work R set: 0.7991 / SU B: 18.038 / SU ML: 0.21 / SU R Cruickshank DPI: 0.1223 / SU Rfree: 0.0575 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2393 1504 4.8 %RANDOM
Rwork0.1985 29885 --
obs0.2004 32068 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 113.71 Å2 / Biso mean: 37.804 Å2 / Biso min: 13.96 Å2
Baniso -1Baniso -2Baniso -3
1--7.94 Å2-0 Å2-0 Å2
2---7.94 Å2-0 Å2
3---15.89 Å2
Refinement stepCycle: final / Resolution: 2.4→26.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6237 0 10 87 6334
Biso mean--49.84 31.71 -
Num. residues----886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196294
X-RAY DIFFRACTIONr_bond_other_d0.0060.026122
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.9668507
X-RAY DIFFRACTIONr_angle_other_deg1.125313973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7235870
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.59524.502211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.272151010
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8821537
X-RAY DIFFRACTIONr_chiral_restr0.0770.21040
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027243
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021302
X-RAY DIFFRACTIONr_mcbond_it1.9352.5593528
X-RAY DIFFRACTIONr_mcbond_other1.9352.5593527
X-RAY DIFFRACTIONr_mcangle_it3.0533.8174382
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A113300.08
12B113300.08
21A119190.06
22C119190.06
31A111310.08
32D111310.08
41B113360.08
42C113360.08
51B117240.06
52D117240.06
61C111540.08
62D111540.08
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 98 -
Rwork0.217 1845 -
all-1943 -
obs--80.79 %
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)
10.7890.19110.27941.59140.44241.96010.01970.1357-0.0877-0.06080.05660.00390.05550.0054-0.07630.0823-0.0001-0.00550.1503-0.02390.0126-5.326417.6827-18.8349
28.5303-2.7439-2.50631.76961.03450.7960.01340.26950.1518-0.00550.0271-0.0403-0.0109-0.0517-0.04050.0658-0.0217-0.00570.1343-0.00520.00537.025428.2165-20.4222
32.6482-0.21470.42990.54350.89051.74080.09550.13750.0476-0.0509-0.0187-0.0383-0.07080.1141-0.07680.1003-0.0348-0.00570.2138-0.00290.04894.456129.9822-10.2384
40.8026-0.15030.41570.759-0.16210.56140.120.0999-0.056-0.0428-0.13840.03810.09140.10.01830.1018-0.0038-0.00740.1453-0.01850.01676.052316.1678-3.4625
52.4711-0.54420.31560.4101-0.36262.2002-0.0073-0.1353-0.03490.0589-0.02850.0725-0.08190.08820.03570.1041-0.0520.03080.1168-0.00240.0276-8.381517.105620.0323
60.67490.6283-0.98967.09692.06942.82560.0926-0.1209-0.01360.2682-0.0015-0.2449-0.04760.2219-0.09120.0544-0.0254-0.03080.14250.00070.03526.212916.034321.7663
70.1218-0.0057-0.32770.02230.13171.50810.1042-0.09140.00220.0096-0.0164-0.0125-0.23240.1417-0.08790.1654-0.0557-0.01750.1132-0.02310.08733.738227.694711.5319
80.7051-0.2933-0.47192.56670.49370.54950.0173-0.1253-0.01160.05410.03680.0444-0.04330.006-0.05410.1108-0.03820.01680.1703-0.00710.0343-1.942125.04564.6693
91.0146-0.00810.55581.86180.00931.8507-0.105-0.17280.09460.11250.1651-0.21050.0473-0.103-0.06010.12230.0228-0.04920.1444-0.02070.04572.8768-13.254118.9479
100.64941.8073-0.29168.4964-2.56181.04530.0234-0.0756-0.03510.27070.0358-0.0007-0.0799-0.1239-0.05910.067-0.0246-0.01840.12550.00970.0397-12.3061-18.437220.496
112.93230.32270.50150.09360.00831.0035-0.09680.06320.15280.10830.04740.00990.1278-0.2340.04940.3262-0.0178-0.00940.1847-0.02110.0115-12.23-14.70089.7824
120.724-0.95240.07573.20280.80050.5270.00850.0396-0.01760.2357-0.0112-0.01340.05960.0190.00270.1066-0.031-0.01570.1470.01340.008-0.7767-24.88593.0077
131.49680.04490.42240.9246-0.21840.6727-0.0336-0.02880.0547-0.11580.02830.0189-0.0154-0.03040.00530.1117-0.0296-0.00820.12980.00650.00293.3677-14.0901-19.6175
140.45960.2134-0.1380.0995-0.05930.2073-0.01750.1753-0.0648-0.00940.0712-0.03130.0047-0.1334-0.05370.1258-0.0031-0.02760.194-0.00440.0554-6.5211-22.8258-12.3909
153.2286-4.8782-0.43517.40240.25245.3670.1011-0.20360.1955-0.12290.396-0.25-0.6009-1.1667-0.49710.17020.1277-0.04460.35110.06960.1624-18.4851.6923-9.859
160.9649-0.3691-0.04960.27040.14080.3341-0.0480.02030.0197-0.1232-0.00420.0395-0.11690.06270.05220.163-0.0261-0.05310.16250.01030.0182-5.707-12.0224-4.4762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 93
2X-RAY DIFFRACTION2A94 - 134
3X-RAY DIFFRACTION3A135 - 177
4X-RAY DIFFRACTION4A178 - 246
5X-RAY DIFFRACTION5B2 - 107
6X-RAY DIFFRACTION6B108 - 134
7X-RAY DIFFRACTION7B135 - 209
8X-RAY DIFFRACTION8B210 - 246
9X-RAY DIFFRACTION9C0 - 94
10X-RAY DIFFRACTION10C95 - 134
11X-RAY DIFFRACTION11C135 - 181
12X-RAY DIFFRACTION12C182 - 246
13X-RAY DIFFRACTION13D1 - 155
14X-RAY DIFFRACTION14D156 - 188
15X-RAY DIFFRACTION15D189 - 207
16X-RAY DIFFRACTION16D208 - 246

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