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- PDB-4nhd: Crystal structure of beta-ketoacyl-ACP synthase III (FabH) from V... -

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Basic information

Entry
Database: PDB / ID: 4nhd
TitleCrystal structure of beta-ketoacyl-ACP synthase III (FabH) from Vibrio Cholerae in complex with Coenzyme A
Components3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 1
KeywordsTRANSFERASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / Vibrio cholerae / 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 / 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 1
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsHou, J. / Zheng, H. / Langner, K. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of beta-ketoacyl-ACP synthase III (FabH) from Vibrio Cholerae in complex with Coenzyme A
Authors: Hou, J. / Zheng, H. / Langner, K. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Sep 20, 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 1
B: 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 1
C: 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 1
D: 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,82318
Polymers136,4034
Non-polymers3,42014
Water22,7351262
1
A: 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 1
C: 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,8808
Polymers68,2022
Non-polymers1,6786
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4820 Å2
ΔGint-29 kcal/mol
Surface area21690 Å2
MethodPISA
2
B: 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 1
D: 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,94310
Polymers68,2022
Non-polymers1,7418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-29 kcal/mol
Surface area21740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.449, 100.248, 132.763
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
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEAA0 - 3163 - 319
21PHEPHEBB0 - 3163 - 319
12PHEPHEAA0 - 3163 - 319
22PHEPHECC0 - 3163 - 319
13LYSLYSAA0 - 3153 - 318
23LYSLYSDD0 - 3153 - 318
14PHEPHEBB0 - 3163 - 319
24PHEPHECC0 - 3163 - 319
15LYSLYSBB0 - 3153 - 318
25LYSLYSDD0 - 3153 - 318
16LYSLYSCC0 - 3153 - 318
26LYSLYSDD0 - 3153 - 318

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 34100.836 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: fabH1, VC2023, VC_2023 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q9KQH5, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Chemical
ChemComp-COA / COENZYME A / Coenzyme A


Mass: 767.534 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1262 / 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: 2.43 Å3/Da / Density % sol: 49.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 0.2M calcium chloride, 20%PEG3350, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9792 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Oct 9, 2013 / 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
ReflectionResolution: 1.78→50 Å / Num. obs: 125028 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 25.2
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.817 / Mean I/σ(I) obs: 2 / Num. unique all: 5576 / % possible all: 87.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.8.0049refinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GYO

2gyo


Resolution: 1.78→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.211 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1957 6293 5 %RANDOM
Rwork0.1702 ---
obs0.1715 124893 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 98.87 Å2 / Biso mean: 26.2697 Å2 / Biso min: 5.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0 Å20 Å2
2---1.44 Å20 Å2
3---2.11 Å2
Refinement stepCycle: LAST / Resolution: 1.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9458 0 201 1262 10921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910022
X-RAY DIFFRACTIONr_bond_other_d0.0060.029541
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.98413645
X-RAY DIFFRACTIONr_angle_other_deg1.067321917
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75151289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.56124.427384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.484151619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3021549
X-RAY DIFFRACTIONr_chiral_restr0.180.21579
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211349
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022214
X-RAY DIFFRACTIONr_mcbond_it1.0261.4425123
X-RAY DIFFRACTIONr_mcbond_other1.0261.4425122
X-RAY DIFFRACTIONr_mcangle_it1.662.1586414
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A191390.06
12B191390.06
21A191190.06
22C191190.06
31A188830.06
32D188830.06
41B193320.05
42C193320.05
51B187900.06
52D187900.06
61C191180.06
62D191180.06
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 480 -
Rwork0.248 8534 -
all-9014 -
obs--96.6 %
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)
12.20061.08530.94391.09760.63582.01910.136-0.194-0.00910.1428-0.12510.0273-0.04110.166-0.01090.0916-0.0319-0.01190.08780.03750.074221.009750.5809-18.0094
20.5831-0.0706-0.02270.63990.00020.93460.03810.0331-0.0701-0.0247-0.0401-0.0024-0.01760.01220.0020.02470.0025-0.0050.0097-0.00010.010910.757750.5242-33.8532
31.10980.5705-0.00981.5292-0.53070.5060.1166-0.1790.04210.2436-0.09210.083-0.09420.0271-0.02450.0759-0.02470.02330.0524-0.00610.00756.238552.7438-18.9598
41.26590.5585-0.89130.4498-0.65851.88130.1315-0.10210.08920.0724-0.05740.0968-0.0822-0.1141-0.07410.0579-0.0084-0.00940.056-0.03090.053529.690730.8739-19.6398
50.50410.02880.13520.6917-0.13491.30770.05070.078-0.0015-0.0672-0.0470.0591-0.08040.035-0.00370.0530.0199-0.02620.022-0.01650.029839.840631.9342-35.6302
61.16190.62070.12831.11420.35011.16860.1082-0.0675-0.1650.142-0.0789-0.02490.06290.0387-0.02930.0573-0.0062-0.03240.03190.00490.044344.000827.2525-20.6339
70.6336-0.1358-0.15080.6250.06440.90590.00080.01590.05010.00150.0007-0.0009-0.03650.0424-0.00150.04830.002-0.00290.0388-0.00030.00455.940669.5526-45.268
81.9111.37751.85431.7633.66018.81570.08580.0123-0.29970.17390.0768-0.17720.41170.2369-0.16260.0619-0.0045-0.02430.05810.03490.072125.331462.122-41.9143
90.97220.12310.45890.3129-0.11441.06460.01470.1771-0.0419-0.11380.0161-0.04290.00320.0439-0.03080.08840.00730.01150.0819-0.01710.01214.126363.4731-59.1958
101.3953-0.29170.42011.88880.62231.63250.14960.1485-0.2731-0.1649-0.15840.29630.1292-0.10970.00890.1080.0587-0.1020.0651-0.0790.140441.72948.6183-49.4026
111.4231-0.79550.28141.3636-0.1591.01070.10320.1463-0.2262-0.1147-0.06250.19570.0124-0.0083-0.04070.07910.0543-0.05860.0617-0.05480.066441.919718.8062-46.8346
121.86220.0637-0.16231.18010.22681.07640.13180.4985-0.0019-0.4336-0.13330.1555-0.01760.06760.00160.22440.133-0.08930.2297-0.0530.041947.084420.2897-61.9025
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 48
2X-RAY DIFFRACTION2A49 - 185
3X-RAY DIFFRACTION3A186 - 316
4X-RAY DIFFRACTION4B0 - 47
5X-RAY DIFFRACTION5B48 - 183
6X-RAY DIFFRACTION6B184 - 316
7X-RAY DIFFRACTION7C1 - 184
8X-RAY DIFFRACTION8C185 - 202
9X-RAY DIFFRACTION9C203 - 316
10X-RAY DIFFRACTION10D1 - 96
11X-RAY DIFFRACTION11D97 - 204
12X-RAY DIFFRACTION12D205 - 316

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