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- PDB-4xox: Structure of beta-ketoacyl-ACP synthase I (FabB) from Vibrio Cholerae -

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Basic information

Entry
Database: PDB / ID: 4xox
TitleStructure of beta-ketoacyl-ACP synthase I (FabB) from Vibrio Cholerae
Components3-oxoacyl-ACP synthase
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / Vibrio cholerae / FabB / beta-ketoacyl-(acyl carrier protein) synthase I
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function
Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain ...Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / 3-oxoacyl-ACP synthase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsHou, J. / Grabowski, M. / Cymborowski, M. / Zheng, H. / Cooper, D.R. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: to be published
Title: Structure of beta-ketoacyl-ACP synthase I (FabB) from Vibrio Cholerae
Authors: Hou, J. / Grabowski, M. / Cymborowski, M. / Zheng, H. / Cooper, D.R. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Data collection
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / 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-ACP synthase
B: 3-oxoacyl-ACP synthase


Theoretical massNumber of molelcules
Total (without water)85,4502
Polymers85,4502
Non-polymers00
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-37 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.756, 88.654, 167.258
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 404 / Label seq-ID: 1 - 404

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsThe biological assembly is a dimer.

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Components

#1: Protein 3-oxoacyl-ACP synthase / beta-ketoacyl-ACP synthase I (FabB)


Mass: 42725.176 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor str. N16961 (bacteria)
Strain: O1 biovar eltor str. N16961 / Gene: CD57_00425, DA44_04160, DA72_05820, KV36_05090 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: A0A071LMG6, UniProt: Q7WUU8*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.38 Å3/Da / Density % sol: 48.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.6 M Ammonium citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97927 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Mar 6, 2013 / Details: MIRRORS
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionRedundancy: 4.9 % / Number: 254989 / Rmerge(I) obs: 0.05 / Χ2: 0.79 / D res high: 2 Å / D res low: 27 Å / Num. obs: 51875 / % possible obs: 94.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
5.412710.0340.7415.2
4.35.4110.0320.7885.7
3.764.310.0350.8965.8
3.423.7610.0390.8675.8
3.173.4210.0430.8275.6
2.993.1710.0480.7465.5
2.842.9910.0520.6635.4
2.712.8410.0660.7795.2
2.612.7110.070.7115.2
2.522.6110.0760.7055
2.442.5210.0830.7564.9
2.372.4410.0860.7294.8
2.312.3710.0910.8044.7
2.252.3110.0980.8054.7
2.22.2510.1080.8394.5
2.152.210.1170.8294.5
2.112.1510.1210.8444.3
2.072.1110.1220.8493.9
2.032.0710.1280.873.5
22.0310.1340.8533.1
ReflectionResolution: 2→27 Å / Num. obs: 51875 / % possible obs: 94.3 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.024 / Rrim(I) all: 0.055 / Χ2: 0.79 / Net I/av σ(I): 26.706 / Net I/σ(I): 16.3 / Num. measured all: 254989
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.033.10.13421250.970.0770.1550.85379
2.03-2.073.50.12822740.9660.0680.1450.8783
2.07-2.113.90.12223140.9750.0610.1370.84985.7
2.11-2.154.30.12123780.9760.0570.1340.84488
2.15-2.24.50.11724190.9750.0540.1290.82989.1
2.2-2.254.50.10824570.9720.0510.120.83990.3
2.25-2.314.70.09824930.9690.0460.1090.80592.3
2.31-2.374.70.09125260.9750.0440.1020.80492.4
2.37-2.444.80.08626200.9780.0420.0970.72996.6
2.44-2.524.90.08326190.980.0410.0930.75696.3
2.52-2.6150.07626770.9770.0370.0850.70597.4
2.61-2.715.20.0726880.9820.0340.0780.71198.2
2.71-2.845.20.06627130.980.0330.0740.77999.3
2.84-2.995.40.05227350.9850.0250.0580.66399.5
2.99-3.175.50.04827420.9870.0230.0530.74699.7
3.17-3.425.60.04327730.9880.020.0470.82799.9
3.42-3.765.80.03927720.9920.0180.0430.867100
3.76-4.35.80.03527930.9940.0160.0380.89699.9
4.3-5.415.70.03228500.9950.0150.0360.788100
5.41-275.20.03429070.9930.0170.0390.74197.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data reduction
MOLREPphasing
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OYT

3oyt


Resolution: 2.01→27 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.689 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1767 2492 4.8 %RANDOM
Rwork0.149 49221 --
obs0.1503 49221 93.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 88.05 Å2 / Biso mean: 26.701 Å2 / Biso min: 10.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2--0.85 Å2-0 Å2
3----0.63 Å2
Refinement stepCycle: final / Resolution: 2.01→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5936 0 0 468 6404
Biso mean---34.28 -
Num. residues----808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0196046
X-RAY DIFFRACTIONr_bond_other_d0.0070.025752
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9558174
X-RAY DIFFRACTIONr_angle_other_deg1.308313242
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145814
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.21824.746236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.193151018
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5251528
X-RAY DIFFRACTIONr_chiral_restr0.1010.2932
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027002
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021310
X-RAY DIFFRACTIONr_mcbond_it0.8671.4843238
X-RAY DIFFRACTIONr_mcbond_other0.8671.4833237
X-RAY DIFFRACTIONr_mcangle_it1.4162.224046
Refine LS restraints NCS

Ens-ID: 1 / Number: 47228 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.009→2.061 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.187 156 -
Rwork0.153 2863 -
all-3019 -
obs--75.53 %
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)
10.48790.0039-0.06240.69540.23470.53930.00930.0497-0.0032-0.0894-0.03080.05920.0106-0.02310.02150.0782-0.0057-0.01460.0553-0.0090.112324.165757.331421.216
20.26330.06230.02150.30910.04420.37210.00620.028-0.0065-0.0431-0.02580.01430.00120.01020.01960.074-0.005-0.0080.0684-0.00860.11332.440558.46821.5231
30.88210.2080.08960.55640.04430.24750.0391-0.0823-0.07780.068-0.0475-0.05330.02770.09880.00840.0943-0.017-0.00920.06350.01780.09434.861147.701636.697
40.7694-0.1511-0.50431.55970.25541.18410.0336-0.041-0.05280.1732-0.04130.12450.05640.01730.00770.0788-0.0225-0.01950.05230.0170.095931.384544.998639.5145
50.6420.20850.33550.58070.0391.1881-0.01960.0619-0.0447-0.07550.0436-0.0626-0.04460.0974-0.0240.0889-0.01870.01220.0639-0.01710.120656.933771.453117.2326
60.49270.1280.23870.64250.23460.9949-0.01120.0428-0.0223-0.05680.0124-0.0231-0.04380.0142-0.00130.079-0.00790.00830.0709-0.00370.123248.236568.616420.8603
74.62080.17980.60864.15820.31774.7814-0.0892-0.14670.3154-0.05030.01590.0272-0.36240.0620.07330.12420.03520.01320.1005-0.00570.145333.169683.834626.6587
81.10970.21640.01261.40510.07531.5572-0.0910.04350.1966-0.06610.01620.0223-0.3649-0.07280.07480.14850.0023-0.02990.0085-0.00310.081346.817688.896722.6789
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 112
2X-RAY DIFFRACTION2A113 - 249
3X-RAY DIFFRACTION3A250 - 358
4X-RAY DIFFRACTION4A359 - 404
5X-RAY DIFFRACTION5B1 - 89
6X-RAY DIFFRACTION6B90 - 258
7X-RAY DIFFRACTION7B259 - 287
8X-RAY DIFFRACTION8B288 - 404

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