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- PDB-4i08: Crystal structure of beta-ketoacyl-acyl carrier protein reductase... -

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Basic information

Entry
Database: PDB / ID: 4i08
TitleCrystal structure of beta-ketoacyl-acyl carrier protein reductase (FabG) from Vibrio cholerae in complex with NADPH
Components3-oxoacyl-[acyl-carrier-protein] reductase FabG
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / Vibrio cholerae / FabG / Rossmann fold / beta-ketoacyl-acyl carrier protein reductase / short chain dehydrogenase / NADP(H)
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / : / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...3-oxoacyl-(acyl-carrier-protein) reductase / : / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesVibrio cholerae O1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.063 Å
AuthorsHou, J. / Chruszcz, M. / Zheng, H. / Osinski, T. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
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
DepositionNov 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 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] reductase FabG
B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,29216
Polymers52,7162
Non-polymers2,57614
Water2,306128
1
A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)110,58432
Polymers105,4324
Non-polymers5,15128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
Buried area22630 Å2
ΔGint-280 kcal/mol
Surface area32370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.941, 63.941, 190.374
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 2 - 248 / Label seq-ID: 5 - 251

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

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] reductase FabG / 3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta- ...3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta-ketoacyl-ACP reductase


Mass: 26358.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 (bacteria) / Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: fabG, VC2021, VC_2021 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL
References: UniProt: Q9KQH7, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 9
Details: 2.7M Ammonium Sulfate, 0.1M Tris-HCl, 2% PEG400, pH 9, VAPOR DIFFUSION, temperature 289K

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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: Mar 18, 2011 / 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: 5.6 % / Av σ(I) over netI: 26.95 / Number: 151910 / Rmerge(I) obs: 0.102 / Χ2: 3.18 / D res high: 2.06 Å / D res low: 50 Å / Num. obs: 27006 / % possible obs: 99.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.595099.910.0495.1846.1
4.445.5999.910.0552.8176
3.884.4499.910.0765.1085.7
3.523.8899.810.0622.8565.7
3.273.5299.910.0853.4635.6
3.083.2710010.0871.9665.7
2.923.0899.910.112.2885.6
2.82.9210010.1311.6065.6
2.692.810010.1511.4495.7
2.62.6999.910.2983.9085.6
2.512.699.910.2412.3065.7
2.442.5199.810.1991.3245.7
2.382.4410010.2761.5955.7
2.322.3899.910.3432.8895.6
2.272.3299.810.4072.6795.6
2.222.2710010.4983.6185.7
2.172.2210010.5163.4995.6
2.132.1710010.5484.9535.5
2.12.1399.910.4831.1245
2.062.110010.8119.724.9
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.52
11K, H, -L20.48
ReflectionResolution: 2.06→50 Å / Num. obs: 27006 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 20.5 Å2 / Rmerge(I) obs: 0.102 / Χ2: 3.18 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.06-2.14.90.81113249.721100
2.1-2.1350.48313841.124199.9
2.13-2.175.50.54813264.9531100
2.17-2.225.60.51613373.4991100
2.22-2.275.70.49813613.6181100
2.27-2.325.60.40713202.679199.8
2.32-2.385.60.34313662.889199.9
2.38-2.445.70.27613631.5951100
2.44-2.515.70.19913231.324199.8
2.51-2.65.70.24113552.306199.9
2.6-2.695.60.29813343.908199.9
2.69-2.85.70.15113491.4491100
2.8-2.925.60.13113681.6061100
2.92-3.085.60.1113362.288199.9
3.08-3.275.70.08713411.9661100
3.27-3.525.60.08513723.463199.9
3.52-3.885.70.06213292.856199.8
3.88-4.445.70.07613645.108199.9
4.44-5.5960.05513582.817199.9
5.59-506.10.04913965.184199.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-3000data collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RRO

3rro


Resolution: 2.063→47.86 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.589 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.041 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.171 1330 4.9 %RANDOM
Rwork0.1526 ---
obs0.1535 26944 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.98 Å2 / Biso mean: 38.6873 Å2 / Biso min: 16.98 Å2
Baniso -1Baniso -2Baniso -3
1-11.87 Å20 Å20 Å2
2--11.87 Å20 Å2
3----23.75 Å2
Refinement stepCycle: LAST / Resolution: 2.063→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3546 0 154 128 3828
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193735
X-RAY DIFFRACTIONr_bond_other_d0.0030.023587
X-RAY DIFFRACTIONr_angle_refined_deg1.3432.0115063
X-RAY DIFFRACTIONr_angle_other_deg0.82538213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8045486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.33124.599137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03615619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7491525
X-RAY DIFFRACTIONr_chiral_restr0.0720.2603
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024208
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02791
Refine LS restraints NCS

Ens-ID: 1 / Number: 14329 / 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: 2.063→2.117 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 95 -
Rwork0.208 1851 -
all-1946 -
obs--98.13 %
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)
12.48720.62510.03591.07491.19913.7432-0.0232-0.03250.1218-0.04850.2037-0.2123-0.03170.1087-0.18040.0811-0.04310.00750.1180.00010.17686.85-13.3812.357
21.6960.9292-0.1441.4179-0.35141.1376-0.21880.30450.1212-0.13080.1649-0.0675-0.23470.15620.05390.1215-0.06980.0170.14510.00840.1302-2.673-16.074-9.556
31.39530.59810.11370.4313-0.2370.5171-0.04870.1465-0.07-0.04830.0621-0.0343-0.010.0428-0.01340.0774-0.0186-0.00110.104-0.0080.1542-6.532-26.452-0.79
41.46730.7165-0.63431.29690.46361.01720.08570.14970.2154-0.00710.00790.0677-0.1595-0.0505-0.09360.0952-0.00760.00350.09030.04270.14-7.855-14.3689.816
52.92980.9807-0.96132.0072-0.18722.2571-0.0106-0.03010.11520.0990.063-0.2696-0.11190.1148-0.05240.1033-0.0531-0.03690.0646-0.0030.18117.811-14.99727.79
61.95080.64560.79970.97220.20371.15710.1347-0.2443-0.0520.2313-0.1654-0.1131-0.04520.08710.03080.169-0.0528-0.03690.0888-0.00310.11370.754-21.77439.808
70.99030.5775-0.05150.4168-0.17880.58020.0943-0.0649-0.01460.1618-0.0681-0.0235-0.09640.002-0.02620.1949-0.0477-0.02880.03840.00650.1556-7.563-23.42829.159
80.81730.03920.15811.30160.57950.32430.05350.0981-0.06260.0936-0.0366-0.08990.00330.0439-0.01680.1009-0.0322-0.02640.06910.00840.1528-0.507-24.90917.864
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 39
2X-RAY DIFFRACTION2A40 - 106
3X-RAY DIFFRACTION3A107 - 175
4X-RAY DIFFRACTION4A176 - 248
5X-RAY DIFFRACTION5B2 - 39
6X-RAY DIFFRACTION6B40 - 106
7X-RAY DIFFRACTION7B107 - 205
8X-RAY DIFFRACTION8B206 - 248

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