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

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Basic information

Entry
Database: PDB / ID: 3tzh
TitleCrystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG)(F187A) 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: 2.1 Å
AuthorsHou, J. / Chruszcz, M. / Zheng, H. / Cooper, D.R. / Osinski, T. / Shumilin, I. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 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 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / database_2 ...audit_author / database_2 / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI ..._audit_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 1.3Feb 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
B: 3-oxoacyl-[acyl-carrier protein] reductase
C: 3-oxoacyl-[acyl-carrier protein] reductase
D: 3-oxoacyl-[acyl-carrier protein] reductase
E: 3-oxoacyl-[acyl-carrier protein] reductase
F: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,16279
Polymers157,6926
Non-polymers2,47073
Water15,637868
1
A: 3-oxoacyl-[acyl-carrier protein] reductase
F: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)106,83356
Polymers105,1284
Non-polymers1,70552
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area17520 Å2
ΔGint-211 kcal/mol
Surface area33720 Å2
MethodPISA
2
B: 3-oxoacyl-[acyl-carrier protein] reductase
E: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)106,64156
Polymers105,1284
Non-polymers1,51352
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
Buried area17310 Å2
ΔGint-197 kcal/mol
Surface area33400 Å2
MethodPISA
3
C: 3-oxoacyl-[acyl-carrier protein] reductase
D: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules

C: 3-oxoacyl-[acyl-carrier protein] reductase
D: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,84946
Polymers105,1284
Non-polymers1,72142
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area16660 Å2
ΔGint-227 kcal/mol
Surface area34030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.341, 380.354, 63.212
Angle α, β, γ (deg.)90.000, 119.860, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-252-

SO4

21A-303-

HOH

31D-987-

HOH

41E-971-

HOH

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Components

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


Mass: 26282.018 Da / Num. of mol.: 6 / Mutation: F187A
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-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 47 / Source method: obtained synthetically
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 868 / 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: 41.26 %
Crystal growMethod: vapor diffusion / pH: 9
Details: 0.1M Tris, 2.3M Ammonium Sulfate, pH 9.0, vapor diffusion

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / 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: 2.9 % / Av σ(I) over netI: 23.9 / Number: 210341 / Rmerge(I) obs: 0.046 / Χ2: 0.92 / D res high: 2.1 Å / D res low: 27 Å / Num. obs: 73135 / % possible obs: 98
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.682797.110.0230.5783.2
4.525.6899.310.0250.5873.1
3.954.529910.0330.9693.2
3.593.9599.610.0421.4153.2
3.333.5999.610.0421.1663.2
3.143.3399.710.0481.0863.2
2.983.1499.910.050.8353.2
2.852.9899.910.0570.8283.2
2.742.8599.810.0680.8243.2
2.652.7410010.0850.8663.2
2.562.6599.810.0960.8193.2
2.492.5699.910.1060.8623.1
2.422.4999.910.110.8422.9
2.362.4299.610.1160.8482.8
2.312.3698.710.1140.8322.6
2.262.3197.910.1060.8622.4
2.222.2695.910.1271.492.3
2.182.2294.210.1010.9452.1
2.142.1890.610.1050.9232
2.12.1488.710.1111.0942
ReflectionResolution: 2.1→50 Å / Num. obs: 73135 / % possible obs: 98 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.046 / Χ2: 0.919 / Net I/σ(I): 13.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1420.11132261.094188.7
2.14-2.1820.10534770.923190.6
2.18-2.222.10.10134350.945194.2
2.22-2.262.30.12736801.49195.9
2.26-2.312.40.10635470.862197.9
2.31-2.362.60.11436870.832198.7
2.36-2.422.80.11637710.848199.6
2.42-2.492.90.1136930.842199.9
2.49-2.563.10.10637170.862199.9
2.56-2.653.20.09637410.819199.8
2.65-2.743.20.08537690.8661100
2.74-2.853.20.06836740.824199.8
2.85-2.983.20.05737270.828199.9
2.98-3.143.20.0537460.835199.9
3.14-3.333.20.04837621.086199.7
3.33-3.593.20.04236491.166199.6
3.59-3.953.20.04237751.415199.6
3.95-4.523.20.03337200.969199
4.52-5.683.10.02536870.587199.3
5.68-273.20.02336520.578197.1

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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: 2.1→27 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 7.669 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1911 3593 5 %RANDOM
Rwork0.157 ---
obs0.1587 71522 95.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.22 Å2 / Biso mean: 28.8813 Å2 / Biso min: 10.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.94 Å20 Å2-0.01 Å2
2--1.05 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10761 0 184 868 11813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01911049
X-RAY DIFFRACTIONr_bond_other_d0.0060.027263
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.97814931
X-RAY DIFFRACTIONr_angle_other_deg1.179317840
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53151503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41824.793411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.084151923
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8351574
X-RAY DIFFRACTIONr_chiral_restr0.0850.21787
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212443
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022051
LS refinement shellResolution: 2.1→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 192 -
Rwork0.162 4027 -
all-4219 -
obs--77.23 %
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)
10.19850.02940.2180.66440.02851.12280.004-0.0108-0.02220.1904-0.053-0.13810.49470.20670.0490.41910.08950.07650.06910.02710.1522-2.6280.196-15.262
20.8938-0.00750.27430.4542-0.18930.34530.2223-0.3918-0.32210.1288-0.0702-0.00030.1559-0.0711-0.15210.3706-0.1228-0.12490.19520.15320.18741.13463.597-32.837
31.2172-0.0652-0.46530.65320.28940.4903-0.1527-0.6491-0.60980.33260.0645-0.20640.22750.32070.08820.31840.1038-0.08090.36970.28050.51-19.705-63.2-9.814
41.07850.2864-0.67960.6180.00260.72990.1522-0.775-0.28190.2821-0.2017-0.3135-0.05470.58320.04950.3335-0.1402-0.13490.59650.17250.2388-17.094-33.639-5.287
50.7310.02020.31970.5974-0.01430.45480.0925-0.242-0.01310.1636-0.0512-0.09040.13-0.0364-0.04130.1857-0.0250.00370.11370.03280.14193.87493.191-37.378
60.26680.10610.16940.6046-0.13561.1281-0.0636-0.045-0.01330.1256-0.1364-0.213-0.05670.3250.20.1698-0.0335-0.06230.1420.10910.22432.43829.806-15.359
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 248
2X-RAY DIFFRACTION2B2 - 248
3X-RAY DIFFRACTION3C2 - 248
4X-RAY DIFFRACTION4D2 - 248
5X-RAY DIFFRACTION5E2 - 248
6X-RAY DIFFRACTION6F2 - 248

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