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- PDB-3u09: Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase ... -

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Basic information

Entry
Database: PDB / ID: 3u09
TitleCrystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92D) from Vibrio cholerae
Components3-oxoacyl-[acyl-carrier-protein] reductase FabG
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / Vibrio cholerae / 3-ketoacyl-(acyl-carrier-protein) reductase / FabG
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
3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsHou, J. / Chruszcz, M. / Zheng, H. / Grabowski, M. / Fratczak, Z. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
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
DepositionSep 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Structure summary
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Apr 6, 2016Group: Database references
Revision 1.4Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 1.5Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.6Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,60120
Polymers52,8322
Non-polymers76918
Water6,305350
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
hetero molecules

A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,20240
Polymers105,6654
Non-polymers1,53736
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area17110 Å2
ΔGint-280 kcal/mol
Surface area34370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.574, 63.574, 191.059
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-347-

HOH

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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: 26416.148 Da / Num. of mol.: 2 / Mutation: G92D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: O1 biovar eltor str. N16961 / Gene: fabG, VC2021, VC_2021 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: Q9KQH7, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 10 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.11 Å3/Da / Density % sol: 41.7 %
Crystal growMethod: vapor diffusion / pH: 9
Details: 0.1M Tris, 2.3M Ammonium Sulfate, 5%Tacsimate, pH 9, vapor diffusion

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 6, 2010 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionRedundancy: 4.6 % / Av σ(I) over netI: 38.05 / Number: 194251 / Rmerge(I) obs: 0.054 / Χ2: 2.03 / D res high: 1.75 Å / D res low: 27 Å / Num. obs: 42687 / % possible obs: 97.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.742799.310.0413.0936.1
3.774.7499.910.0392.8066.3
3.293.7799.710.0452.9686.3
2.993.2910010.052.8586
2.782.9999.910.0552.6125.4
2.612.7899.810.0622.4234.8
2.482.6199.710.0682.434.3
2.372.4898.710.0762.274
2.282.3798.510.082.023.8
2.22.2896.810.0922.0193.8
2.142.295.710.0971.8173.7
2.072.1494.710.1131.6423.8
2.022.0794.710.121.3623.9
1.972.0294.710.1531.2374
1.931.9795.310.1951.2124
1.891.9396.110.2351.24
1.851.8995.710.2770.9484.1
1.811.8594.610.3340.8574.2
1.781.8195.310.3610.8224.1
1.751.7895.810.420.7234.1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.833
11K, H, -L20.167
ReflectionResolution: 1.75→27 Å / Num. obs: 42687 / % possible obs: 97.2 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.054 / Χ2: 2.033 / Net I/σ(I): 20.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.75-1.784.10.4220780.723195.8
1.78-1.814.10.36120980.822195.3
1.81-1.854.20.33420700.857194.6
1.85-1.894.10.27720740.948195.7
1.89-1.9340.23521451.2196.1
1.93-1.9740.19520561.212195.3
1.97-2.0240.15320531.237194.7
2.02-2.073.90.1220911.362194.7
2.07-2.143.80.11320711.642194.7
2.14-2.23.70.09721251.817195.7
2.2-2.283.80.09220912.019196.8
2.28-2.373.80.0821602.02198.5
2.37-2.4840.07621792.27198.7
2.48-2.614.30.06821852.43199.7
2.61-2.784.80.06221832.423199.8
2.78-2.995.40.05522002.612199.9
2.99-3.2960.0521872.8581100
3.29-3.776.30.04522052.968199.7
3.77-4.746.30.03922062.806199.9
4.74-276.10.04122303.093199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
DMphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→27 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 3.859 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.187 2259 5.3 %RANDOM
Rwork0.1598 ---
obs0.1613 42619 97.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.83 Å2 / Biso mean: 27.0196 Å2 / Biso min: 13.32 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å20 Å2
2---1.85 Å20 Å2
3---3.7 Å2
Refinement stepCycle: LAST / Resolution: 1.75→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3613 0 50 350 4013
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193711
X-RAY DIFFRACTIONr_bond_other_d0.0030.022434
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9755019
X-RAY DIFFRACTIONr_angle_other_deg1.02735973
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3515502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56924.752141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.39115644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0871524
X-RAY DIFFRACTIONr_chiral_restr0.0730.2597
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024182
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02702
LS refinement shellResolution: 1.749→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 140 -
Rwork0.23 2861 -
all-3001 -
obs--93.69 %
Refinement TLS params.Method: refined / Origin x: 2.654 Å / Origin y: 19.766 Å / Origin z: -0.099 Å
111213212223313233
T0.132 Å2-0.0407 Å20.02 Å2-0.0751 Å2-0.0211 Å2--0.0163 Å2
L0.7303 °20.4121 °2-0.0628 °2-0.4501 °2-0.0521 °2--0.5265 °2
S0.0861 Å °0.1169 Å °-0.0095 Å °0.1685 Å °-0.0368 Å °0.0458 Å °0.0509 Å °-0.054 Å °-0.0493 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 248
2X-RAY DIFFRACTION1B2 - 248

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