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

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Basic information

Entry
Database: PDB / ID: 3tzc
TitleCrystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(Y155F) 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 / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 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
C: 3-oxoacyl-[acyl-carrier protein] reductase
D: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,07215
Polymers105,3684
Non-polymers1,70411
Water2,918162
1
C: 3-oxoacyl-[acyl-carrier protein] reductase
D: 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)107,07215
Polymers105,3684
Non-polymers1,70411
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area12250 Å2
ΔGint-182 kcal/mol
Surface area35370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.353, 62.353, 383.381
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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


Mass: 26342.113 Da / Num. of mol.: 4 / Mutation: Y155F
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-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growMethod: vapor diffusion / pH: 8.5
Details: 0.1M Tris, 2.3M Ammonium Sulfate, pH 8.5, 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: 3.3 % / Av σ(I) over netI: 15.44 / Number: 100742 / Rmerge(I) obs: 0.108 / Χ2: 1.61 / D res high: 2.45 Å / D res low: 50 Å / Num. obs: 30294 / % possible obs: 98.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.655095.210.0563.4863.3
5.286.6597.610.0662.5613.6
4.615.2897.610.0642.5333.1
4.194.6194.610.0652.6362.8
3.894.1996.510.0752.3163
3.663.8995.810.0862.2933
3.483.6696.510.0962.2373
3.323.4896.210.1181.9663.2
3.23.3298.510.1451.633.5
3.093.299.510.181.5193.6
2.993.0999.110.1961.4353.6
2.92.9998.710.2141.3533.6
2.832.999.610.2731.1313.7
2.762.8399.910.2871.0633.7
2.72.7699.910.3290.9873.8
2.642.799.910.3820.8683.7
2.592.6410010.4180.7823.6
2.542.5999.910.4220.7123.3
2.492.5499.910.4510.7063
2.452.4999.910.4350.6762.5
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.709
11K, H, -L20.291
ReflectionResolution: 2.45→50.01 Å / Num. obs: 30294 / % possible obs: 98.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.108 / Χ2: 1.605 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.45-2.492.50.43516070.676199.9
2.49-2.5430.45114760.706199.9
2.54-2.593.30.42215550.712199.9
2.59-2.643.60.41815140.7821100
2.64-2.73.70.38215660.868199.9
2.7-2.763.80.32915120.987199.9
2.76-2.833.70.28715651.063199.9
2.83-2.93.70.27314701.131199.6
2.9-2.993.60.21415641.353198.7
2.99-3.093.60.19615091.435199.1
3.09-3.23.60.1815001.519199.5
3.2-3.323.50.14515231.63198.5
3.32-3.483.20.11815161.966196.2
3.48-3.6630.09614832.237196.5
3.66-3.8930.08614772.293195.8
3.89-4.1930.07514692.316196.5
4.19-4.612.80.06514362.636194.6
4.61-5.283.10.06415232.533197.6
5.28-6.653.60.06615122.561197.6
6.65-503.30.05615173.486195.2

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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: 2.45→50 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 10.904 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / 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
Rfree0.2272 1524 5 %RANDOM
Rwork0.1882 ---
obs0.1902 30184 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.43 Å2 / Biso mean: 40.3658 Å2 / Biso min: 18.94 Å2
Baniso -1Baniso -2Baniso -3
1--19.18 Å20 Å20 Å2
2---19.18 Å20 Å2
3---38.36 Å2
Refinement stepCycle: LAST / Resolution: 2.45→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6287 0 77 162 6526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196471
X-RAY DIFFRACTIONr_bond_other_d0.0050.024189
X-RAY DIFFRACTIONr_angle_refined_deg1.5361.9758757
X-RAY DIFFRACTIONr_angle_other_deg1.216310256
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8695881
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94124.071226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.333151043
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3091543
X-RAY DIFFRACTIONr_chiral_restr0.1090.21060
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027281
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021253
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 89 -
Rwork0.274 2152 -
all-2241 -
obs--97.82 %
Refinement TLS params.Method: refined / Origin x: -1.273 Å / Origin y: 3.229 Å / Origin z: 0.935 Å
111213212223313233
T0.114 Å2-0.0261 Å20.0115 Å2-0.1155 Å2-0.0019 Å2--0.004 Å2
L0.3237 °2-0.1367 °2-0.0387 °2-0.1052 °20.007 °2--0.088 °2
S0.0027 Å °0.0066 Å °-0.0117 Å °-0.0018 Å °0.0061 Å °0.0131 Å °-0.0048 Å °-0.0373 Å °-0.0088 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 246
2X-RAY DIFFRACTION1B2 - 246
3X-RAY DIFFRACTION1C2 - 246
4X-RAY DIFFRACTION1D2 - 246

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