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

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Basic information

Entry
Database: PDB / ID: 3tzk
TitleCrystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(G92A) from Vibrio cholerae
Components3-oxoacyl-[acyl-carrier protein] reductase
KeywordsOXIDOREDUCTASE / Vibrio cholerae / 3-ketoacyl-(acyl-carrier-protein) reductase / FabG / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsHou, J. / Chruszcz, M. / Zheng, H. / Grabowski, M. / Domagalski, M. / 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 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Feb 3, 2016Group: Database references
Revision 1.3Nov 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 1.4Apr 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 1.5Feb 28, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,41721
Polymers52,7442
Non-polymers67219
Water5,747319
1
A: 3-oxoacyl-[acyl-carrier protein] reductase
B: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)106,83342
Polymers105,4894
Non-polymers1,34538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z1
Buried area16730 Å2
ΔGint-256 kcal/mol
Surface area33910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.290, 63.290, 190.431
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-313-

HOH

21A-314-

HOH

31B-326-

HOH

41B-340-

HOH

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Components

#1: Protein 3-oxoacyl-[acyl-carrier protein] reductase


Mass: 26372.139 Da / Num. of mol.: 2 / Mutation: G92A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: MJ-1236 / Gene: VC2021, VCD_002346 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL
References: UniProt: C3NP04, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 12 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.09 Å3/Da / Density % sol: 41.08 %
Crystal growMethod: vapor diffusion / pH: 9
Details: 0.1M Tris, 2.4M Ammonium Sulfate, pH 9.0, 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 210r / 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: 9.2 % / Av σ(I) over netI: 43.96 / Number: 366074 / Rmerge(I) obs: 0.051 / Χ2: 0.9 / D res high: 1.8 Å / D res low: 27 Å / Num. obs: 39838 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.882799.410.0331.679.2
3.874.8899.810.0251.0589.6
3.393.8799.910.0281.0459.6
3.083.3910010.0341.0019.6
2.863.0899.910.0410.9479.6
2.692.8610010.0530.9519.6
2.552.6910010.0660.9229.6
2.442.5510010.0760.9119.6
2.352.4410010.0940.8849.6
2.272.3510010.1060.8889.6
2.22.2710010.1220.8819.6
2.132.210010.1380.8499.6
2.082.1310010.1680.8459.6
2.032.0810010.1990.8159.6
1.982.0310010.2460.7769.5
1.941.9810010.3130.7229.4
1.91.9410010.350.698.6
1.861.910010.4290.6368
1.831.8610010.4860.627.5
1.81.8310010.5190.5796.7
ReflectionResolution: 1.8→50 Å / Num. obs: 39838 / % possible obs: 99.9 % / Redundancy: 9.2 % / Rmerge(I) obs: 0.051 / Χ2: 0.896 / Net I/σ(I): 14
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.836.70.51919450.5791100
1.83-1.867.50.48620330.621100
1.86-1.980.42919360.6361100
1.9-1.948.60.3519860.691100
1.94-1.989.40.31320260.7221100
1.98-2.039.50.24619950.7761100
2.03-2.089.60.19919620.8151100
2.08-2.139.60.16820060.8451100
2.13-2.29.60.13819990.8491100
2.2-2.279.60.12219860.8811100
2.27-2.359.60.10619860.8881100
2.35-2.449.60.09419960.8841100
2.44-2.559.60.07619780.9111100
2.55-2.699.60.06619880.9221100
2.69-2.869.60.05319940.9511100
2.86-3.089.60.04119780.947199.9
3.08-3.399.60.03420091.0011100
3.39-3.879.60.02819961.045199.9
3.87-4.889.60.02520281.058199.8
4.88-279.20.03320111.67199.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
DMphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.345 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2107 1997 5 %RANDOM
Rwork0.1648 ---
obs0.1671 39785 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.15 Å2 / Biso mean: 30.8079 Å2 / Biso min: 16.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.05 Å20 Å2
2---0.1 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3603 0 47 319 3969
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193691
X-RAY DIFFRACTIONr_bond_other_d0.0010.022427
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9754990
X-RAY DIFFRACTIONr_angle_other_deg0.89835960
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4745500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.16724.71138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.43115647
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3021524
X-RAY DIFFRACTIONr_chiral_restr0.0820.2595
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024153
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02695
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 130 -
Rwork0.219 2746 -
all-2876 -
obs--99.76 %
Refinement TLS params.Method: refined / Origin x: -18.39 Å / Origin y: 7.635 Å / Origin z: 0.046 Å
111213212223313233
T0.1774 Å20.0136 Å2-0.0012 Å2-0.2164 Å20.0328 Å2--0.0127 Å2
L0.901 °20.2644 °2-0.0043 °2-0.3275 °2-0.0728 °2--0.7249 °2
S0.0981 Å °0.1674 Å °0.0501 Å °0.0739 Å °-0.0685 Å °-0.0274 Å °-0.044 Å °0.092 Å °-0.0296 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 248
2X-RAY DIFFRACTION1B2 - 248

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