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- PDB-4wk6: Crystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase ... -

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Basic information

Entry
Database: PDB / ID: 4wk6
TitleCrystal structure of 3-ketoacyl-(acyl-carrier-protein) reductase (FabG) (G141A) from Vibrio cholerae in complex with NADPH
Components3-oxoacyl-[acyl-carrier protein] reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / FabG / acyl carrier protein / Cell Plasma
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Chem-NDP / :
Function and homology information
Biological speciesVibrio cholerae 12129
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 Å
AuthorsHou, J. / Zheng, H. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272200700058C United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
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
DepositionOct 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Data collection
Revision 1.2Nov 25, 2015Group: Database references
Revision 1.3Feb 3, 2016Group: Database references
Revision 1.4Sep 27, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.5Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.6Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
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
Revision 1.7Dec 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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] 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)108,7099
Polymers105,4894
Non-polymers3,2205
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13480 Å2
ΔGint-81 kcal/mol
Surface area34860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.904, 110.337, 117.482
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: _ / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEAA4 - 2467 - 249
21PHEPHEBB4 - 2467 - 249
12PHEPHEAA4 - 2467 - 249
22PHEPHECC4 - 2467 - 249
13PHEPHEAA4 - 2467 - 249
23PHEPHEDD4 - 2467 - 249
14GLNGLNBB3 - 2466 - 249
24GLNGLNCC3 - 2466 - 249
15GLNGLNBB3 - 2466 - 249
25GLNGLNDD3 - 2466 - 249
16GLNGLNCC3 - 2466 - 249
26GLNGLNDD3 - 2466 - 249

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 26372.141 Da / Num. of mol.: 4 / Mutation: G141A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae 12129(1) (bacteria) / Gene: VCG_002050 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon plus
References: UniProt: C2CCH9, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.17 M Ammonium Acetate,0.085 M Sodium Citrate:HCl,25.5% (w/v) PEG 4000,15% (v/v) Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 23, 2014
RadiationMonochromator: Diamond 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionRedundancy: 6 % / Number: 312294 / Rmerge(I) obs: 0.077 / Χ2: 1.35 / D res high: 2.2 Å / D res low: 27 Å / Num. obs: 52121 / % possible obs: 98.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
5.952710.0471.8535.5
4.735.9510.0511.7846
4.144.7310.0562.2395.9
3.764.1410.0662.2466
3.493.7610.0711.9696.1
3.283.4910.0811.7626.1
3.123.2810.1011.466.2
2.993.1210.1191.3566.2
2.872.9910.1421.3556.2
2.772.8710.171.2666.2
2.682.7710.2081.176.2
2.612.6810.2561.0696.2
2.542.6110.281.0216.2
2.482.5410.3210.9346.2
2.422.4810.3780.8966.1
2.372.4210.4080.8756
2.322.3710.4470.8755.9
2.282.3210.4950.8435.7
2.242.2810.5270.8615.5
2.22.2410.6060.8065.4
ReflectionResolution: 2.2→27 Å / Num. obs: 52121 / % possible obs: 98.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.034 / Rrim(I) all: 0.084 / Χ2: 1.346 / Net I/av σ(I): 28 / Net I/σ(I): 7.4 / Num. measured all: 312294
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.245.40.60624310.8810.2680.6640.80693.9
2.24-2.285.50.52724210.9060.2330.5780.86193.6
2.28-2.325.70.49524650.9180.2190.5430.84394.7
2.32-2.375.90.44725020.9320.1970.490.87596.7
2.37-2.4260.40825700.9440.180.4470.87598.4
2.42-2.486.10.37826160.9530.1670.4140.89699.8
2.48-2.546.20.32125900.9730.1410.3510.934100
2.54-2.616.20.2826190.9720.1220.3061.021100
2.61-2.686.20.25626110.980.1120.281.069100
2.68-2.776.20.20826090.9840.090.2271.17100
2.77-2.876.20.1726200.9890.0740.1861.266100
2.87-2.996.20.14226320.990.0620.1551.355100
2.99-3.126.20.11926240.9940.0510.1291.356100
3.12-3.286.20.10126350.9940.0440.111.46100
3.28-3.496.10.08126340.9950.0350.0891.76299.7
3.49-3.766.10.07126460.9960.0310.0771.969100
3.76-4.1460.06626590.9960.0290.0722.246100
4.14-4.735.90.05626780.9970.0240.0612.23999.7
4.73-5.9560.05127160.9980.0220.0551.784100
5.95-275.50.04728430.9980.0220.0521.85399.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data reduction
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.21→27 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.947 / SU B: 20.048 / SU ML: 0.222 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 2512 4.8 %RANDOM
Rwork0.2091 49545 --
obs0.2107 49545 98.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.74 Å2 / Biso mean: 65.28 Å2 / Biso min: 36.81 Å2
Baniso -1Baniso -2Baniso -3
1-4.64 Å20 Å2-0 Å2
2---6.09 Å20 Å2
3---1.45 Å2
Refinement stepCycle: final / Resolution: 2.21→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6704 0 128 99 6931
Biso mean--77.53 54.65 -
Num. residues----953
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196908
X-RAY DIFFRACTIONr_bond_other_d0.0070.026593
X-RAY DIFFRACTIONr_angle_refined_deg1.6011.9849382
X-RAY DIFFRACTIONr_angle_other_deg1.245315039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9675947
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35224.746236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.839151065
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4221539
X-RAY DIFFRACTIONr_chiral_restr0.0860.21136
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027968
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021451
X-RAY DIFFRACTIONr_mcbond_it2.3833.133806
X-RAY DIFFRACTIONr_mcbond_other2.3833.1293805
X-RAY DIFFRACTIONr_mcangle_it3.6754.6794744
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A121550.11
12B121550.11
21A121390.11
22C121390.11
31A111260.09
32D111260.09
41B126720.09
42C126720.09
51B115790.09
52D115790.09
61C116830.07
62D116830.07
LS refinement shellResolution: 2.205→2.262 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 165 -
Rwork0.344 3163 -
all-3328 -
obs--86.22 %
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)
14.4284-0.08910.15254.0831-1.47384.10380.07380.65770.3879-0.5354-0.0114-0.1341-0.2054-0.0474-0.06240.76120.04110.06050.46410.08310.04425.7134.4544.023
21.7095-1.1195-0.41192.4650.59361.23620.03960.24830.0563-0.4158-0.05750.188-0.0889-0.05180.01790.66090.0095-0.09770.31850.02630.0354-6.36532.82716.085
31.33060.56611.24863.89991.09442.5376-0.12180.13440.267-0.3132-0.0922-0.0868-0.3126-0.02240.2140.4852-0.00380.0120.30890.02520.0667.57633.96723.279
42.6784-0.1833-0.99884.6646-0.48754.3669-0.0330.0075-0.10940.02420.2443-0.5220.44840.5341-0.21130.36070.12350.00470.3218-0.0980.100324.58311.9132.297
52.00861.4774-1.25983.0416-1.15421.2959-0.0980.0584-0.1036-0.11460.0910.04510.1769-0.00030.0070.45570.0128-0.00950.3257-0.02520.073610.65316.65939.878
60.67940.2410.89582.44410.5631.25510.1131-0.057-0.1056-0.13130.03220.00620.2531-0.0505-0.14530.602-0.00750.02160.3519-0.00450.03646.00410.88222.891
71.93010.274-0.40620.9045-0.05250.9099-0.1123-0.1655-0.1080.2220.03980.09060.17330.02960.07250.4823-0.00520.03330.3318-0.00150.0234-10.60215.1157.792
85.94320.6046-0.01460.07020.01770.0578-0.0705-0.00190.3432-0.00470.02730.06140.02420.08520.04320.4222-0.0327-0.00510.4046-0.03090.1432-5.53218.21745.583
91.25890.1420.49773.5407-0.01472.5297-0.02230.02270.06930.1427-0.0818-0.1999-0.35550.0550.10420.4639-0.04730.0190.3498-0.01770.0794-12.56327.57347.303
103.81441.2457-0.68442.5335-1.97272.9953-0.00690.31480.1535-0.04770.33810.6544-0.1866-0.6637-0.33130.40480.0683-0.08670.45210.08170.2214-34.53933.13129.881
111.2815-0.3959-0.14351.8154-0.75422.69540.04960.1733-0.0159-0.10970.06340.2559-0.0673-0.1071-0.1130.53840.0189-0.07710.3526-0.01450.0472-20.76533.25827.532
121.1325-0.48630.60884.61761.00441.85350.11130.2265-0.0875-0.2839-0.01930.42580.1829-0.1792-0.0920.4871-0.0367-0.03850.395-0.03730.0815-21.98418.56434.411
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 94
2X-RAY DIFFRACTION2A95 - 175
3X-RAY DIFFRACTION3A176 - 246
4X-RAY DIFFRACTION4B3 - 90
5X-RAY DIFFRACTION5B91 - 181
6X-RAY DIFFRACTION6B182 - 246
7X-RAY DIFFRACTION7C3 - 134
8X-RAY DIFFRACTION8C135 - 170
9X-RAY DIFFRACTION9C171 - 246
10X-RAY DIFFRACTION10D3 - 101
11X-RAY DIFFRACTION11D102 - 196
12X-RAY DIFFRACTION12D197 - 246

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