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- PDB-5kp2: Beta-ketoacyl-ACP synthase III -2 (FabH2) (C113A) from Vibrio Cho... -

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Basic information

Entry
Database: PDB / ID: 5kp2
TitleBeta-ketoacyl-ACP synthase III -2 (FabH2) (C113A) from Vibrio Cholerae cocrystallized with octanoyl-CoA: hydrolzed ligand
Components3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / FabH / beta-ketoacyl-acyl carrier protein synthase III
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / OCTANOIC ACID (CAPRYLIC ACID) / Beta-ketoacyl-[acyl-carrier-protein] synthase III 2
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsHou, J. / Zheng, H. / Grabowski, M. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 2items
OrganizationGrant numberCountry
Department of Health & Human Services (HHS)HHSN272200700058C United States
Department of Health & Human Services (HHS)HHSN272201200026C United States
CitationJournal: To Be Published
Title: Beta-ketoacyl-ACP synthase III -2 (FabH2) (C113A) from Vibrio Cholerae soaked with octanoyl-CoA: hydrolzed ligand
Authors: Center for Structural Genomics of Infectious Diseases (CSGID) / Hou, J. / Zheng, H. / Grabowski, M. / Anderson, W.F.
History
DepositionJul 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Data collection / Database references
Category: database_2 / diffrn_radiation_wavelength / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Apr 13, 2022Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Oct 4, 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-[acyl-carrier-protein] synthase 3 protein 2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9844
Polymers78,0722
Non-polymers9122
Water6,828379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-28 kcal/mol
Surface area23580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.670, 61.242, 71.524
Angle α, β, γ (deg.)90.00, 94.67, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 3 - 358 / Label seq-ID: 3 - 358

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2 / 3-oxoacyl-[acyl-carrier-protein] synthase III protein 2 / Beta-ketoacyl-ACP synthase III 2 / KAS III 2


Mass: 39036.117 Da / Num. of mol.: 2 / Mutation: C113A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria)
Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: fabH2, VC_A0751 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q9KLJ3, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Chemical ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-OCA / OCTANOIC ACID (CAPRYLIC ACID) / Caprylic acid


Mass: 144.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H16O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 2.39 Å3/Da / Density % sol: 48.53 % / Mosaicity: 0.397 °
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7 / Details: 0.2 M ammonium phosphate, 20% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 22, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→27 Å / Num. obs: 48065 / % possible obs: 96.7 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.067 / Rrim(I) all: 0.121 / Χ2: 1.518 / Net I/av σ(I): 12.752 / Net I/σ(I): 6.9 / Num. measured all: 141501
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.032.90.413196.9
2.03-2.072.90.345198
2.07-2.112.90.311198.4
2.11-2.152.90.27198.5
2.15-2.22.90.241198.1
2.2-2.252.90.218198.4
2.25-2.312.90.201198
2.31-2.372.90.186197.9
2.37-2.4430.163197.6
2.44-2.522.90.154197.6
2.52-2.612.90.132197.4
2.61-2.7130.122197.2
2.71-2.8430.112196.9
2.84-2.9930.099196.6
2.99-3.1730.088196.1
3.17-3.4230.086195.7
3.42-3.7630.081195.2
3.76-4.32.90.071194.5
4.3-5.4130.06193.7
5.41-2730.05191.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data collection
HKL-3000data scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WZU

4wzu


Resolution: 2→27 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.917 / SU B: 9.361 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.202 / ESU R Free: 0.162 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22095 2360 4.9 %RANDOM
Rwork0.19386 ---
obs0.19521 45559 96.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.408 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å2-0.77 Å2
2---0.57 Å2-0 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 2→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5283 0 58 379 5720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195490
X-RAY DIFFRACTIONr_bond_other_d0.0030.025204
X-RAY DIFFRACTIONr_angle_refined_deg1.3391.9527486
X-RAY DIFFRACTIONr_angle_other_deg0.987311895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9595723
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.63523.909220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.51115834
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8051532
X-RAY DIFFRACTIONr_chiral_restr0.0730.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026356
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021267
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3321.1762880
X-RAY DIFFRACTIONr_mcbond_other0.3321.1762879
X-RAY DIFFRACTIONr_mcangle_it0.5941.7633604
X-RAY DIFFRACTIONr_mcangle_other0.5941.7633605
X-RAY DIFFRACTIONr_scbond_it0.4221.3142610
X-RAY DIFFRACTIONr_scbond_other0.4221.3152611
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.7161.9513882
X-RAY DIFFRACTIONr_long_range_B_refined4.97810.5686175
X-RAY DIFFRACTIONr_long_range_B_other4.86410.2156053
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 41130 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.04 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 165 -
Rwork0.242 3370 -
obs--97.12 %
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)
11.49540.217-0.0131.0362-0.68672.5846-0.01010.2936-0.1787-0.17160.0197-0.3685-0.01840.2562-0.00960.0462-0.00680.05020.0912-0.07410.235534.8143-11.788113.7579
21.3090.09540.05630.96380.30521.2570.01510.1112-0.097-0.06990.0023-0.03060.03720.0705-0.01750.02750.0204-0.00720.0264-0.01650.161621.6568-7.356919.5995
30.93310.21260.21341.2704-0.30741.0822-0.03970.20540.0149-0.1040.002-0.1128-0.09440.09410.03770.0302-0.00050.01780.0669-0.01290.149526.14551.095115.345
41.59870.13861.15411.5143-1.568110.3067-0.05510.11980.10270.0534-0.0605-0.2044-0.23620.02320.11550.0158-0.0117-0.00280.03180.00010.176637.84378.826523.51
50.94390.16780.211.046-0.35390.9410.00190.1913-0.1291-0.07710.0393-0.25470.0690.1505-0.04120.01080.00850.02150.0591-0.04370.201938.0247-7.625621.3894
61.1340.1760.63890.8220.56493.01980.00340.0650.0663-0.1592-0.06010.20380.0646-0.23210.05670.05750.0084-0.0070.0370.01820.14931.330311.650613.6283
70.9436-0.14660.11530.8254-0.19611.17440.03350.04080.0347-0.0724-0.0078-0.0124-0.03170.0026-0.02570.02950.01010.01740.0195-0.0020.154113.98426.899919.0794
81.00880.1659-0.34810.95450.19430.9425-0.00740.1648-0.0741-0.07840.01080.04570.1391-0.091-0.00340.04860.0066-0.01160.04650.00130.1586.9469-4.66217.6522
90.4030.3856-0.4041.1220.31891.63690.016-0.01880.04160.017-0.03860.2230.0262-0.14870.02260.0072-0.0049-0.0020.04670.0260.1818-5.49974.453725.3659
100.4068-0.05980.00940.95030.11621.40190.02750.09950.0451-0.11360.01690.0813-0.1655-0.083-0.04450.03250.0186-0.00630.06470.00760.18043.62449.908416.9226
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 68
2X-RAY DIFFRACTION2A69 - 155
3X-RAY DIFFRACTION3A156 - 211
4X-RAY DIFFRACTION4A212 - 240
5X-RAY DIFFRACTION5A241 - 359
6X-RAY DIFFRACTION6B2 - 68
7X-RAY DIFFRACTION7B69 - 160
8X-RAY DIFFRACTION8B161 - 236
9X-RAY DIFFRACTION9B237 - 302
10X-RAY DIFFRACTION10B303 - 359

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