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- PDB-3rsh: Structure of 3-ketoacyl-(acyl-carrier-protein)reductase (FabG) fr... -

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Basic information

Entry
Database: PDB / ID: 3rsh
TitleStructure of 3-ketoacyl-(acyl-carrier-protein)reductase (FabG) from Vibrio cholerae O1 complexed with NADP+ (space group P62)
Components3-oxoacyl-[acyl-carrier protein] reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / OXIREDUCTASE / FabG / acyl carrier protein / Cell plasma
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / : / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsHou, J. / Chruszcz, M. / Cooper, D.R. / Grabowski, M. / Zheng, H. / Osinski, T. / Shumilin, I. / Anderson, W. / 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
DepositionMay 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 2, 2012Group: Structure summary
Revision 1.3Nov 25, 2015Group: Database references
Revision 1.4Mar 23, 2016Group: Database references
Revision 1.5Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_special_symmetry / 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 1.6Sep 13, 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
B: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,38425
Polymers52,7162
Non-polymers2,66823
Water2,684149
1
A: 3-oxoacyl-[acyl-carrier protein] reductase
B: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)110,76850
Polymers105,4324
Non-polymers5,33546
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area22380 Å2
ΔGint-318 kcal/mol
Surface area32770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.776, 63.776, 190.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-253-

SO4

21B-254-

SO4

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERVALVAL4AA2 - 1805 - 183
21SERSERVALVAL4BB2 - 1805 - 183
12ASNASNALAALA4AA181 - 210184 - 213
22ASNASNALAALA4BB181 - 210184 - 213
13GLYGLYILEILE1AA211 - 248214 - 251
23GLYGLYILEILE1BB211 - 248214 - 251

NCS ensembles :
ID
1
2
3

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 26358.113 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VCD_002346 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codonplus
References: UniProt: C3NP04, UniProt: Q9KQH7*PLUS, 3-oxoacyl-[acyl-carrier-protein] reductase

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Non-polymers , 5 types, 172 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 0.1M Tris pH9.0, 2.6M Ammonium Sulfate, 5% Tacsimate, VAPOR DIFFUSION, HANGING DROP, 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
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.536
11-H-K, K, -L20.464
ReflectionResolution: 1.95→50 Å / Num. all: 31596 / Num. obs: 31596 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.063 / Net I/σ(I): 26.4
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1606 / Rsym value: 0.593 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
REFMAC5.5.0109refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OP4

3op4


Resolution: 1.95→50.01 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.967 / SU B: 4.082 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15568 1611 5.1 %RANDOM
Rwork0.13255 ---
all0.13377 29935 --
obs0.13377 29935 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.466 Å2
Baniso -1Baniso -2Baniso -3
1-11.1 Å20 Å20 Å2
2--11.1 Å20 Å2
3----22.2 Å2
Refinement stepCycle: LAST / Resolution: 1.95→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3570 0 167 149 3886
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223756
X-RAY DIFFRACTIONr_bond_other_d0.0010.022438
X-RAY DIFFRACTIONr_angle_refined_deg1.2612.0135087
X-RAY DIFFRACTIONr_angle_other_deg0.85735968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.545487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3924.478134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56715629
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2121525
X-RAY DIFFRACTIONr_chiral_restr0.0690.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024122
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02705
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_it0.511.52407
X-RAY DIFFRACTIONr_mcbond_other0.1371.51026
X-RAY DIFFRACTIONr_mcangle_it0.8923818
X-RAY DIFFRACTIONr_scbond_it1.47631349
X-RAY DIFFRACTIONr_scangle_it2.4294.51269
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
12188MEDIUM POSITIONAL0.20.5
12188MEDIUM THERMAL0.422
2278MEDIUM POSITIONAL0.30.5
2278MEDIUM THERMAL0.262
3465TIGHT POSITIONAL0.020.05
3465TIGHT THERMAL0.10.5
LS refinement shellResolution: 1.949→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.232 126 -
Rwork0.147 2203 -
obs--98.52 %
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)
10.87890.2939-0.83551.8307-0.46622.7119-0.13460.1623-0.0775-0.09850.1770.09060.3422-0.2101-0.04240.0542-0.0548-0.0170.1226-0.03260.1647-6.16111.863-2.209
21.11310.1501-0.07860.65720.17310.7518-0.00520.2176-0.0218-0.02510.05240.02850.0442-0.1044-0.04730.0051-0.0044-0.0040.106-0.00280.13567.12722.941-4.569
30.6760.21140.42390.9273-0.30080.69230.07640.113-0.07210.0264-0.0372-0.00330.10870.0323-0.03920.04340.0010.00550.0682-0.02410.14956.92816.5039.435
41.6023-0.0309-0.31981.34070.95754.04250.0778-0.1172-0.04550.1378-0.09370.1160.1923-0.15320.0160.1141-0.06910.05410.0521-0.00270.1395-6.71315.63834.633
50.99330.7629-0.02711.13610.19140.53610.1413-0.1146-0.00180.2783-0.11130.0380.0368-0.0083-0.030.1478-0.050.01650.0239-0.0050.1458.15523.18833.388
60.8264-0.29180.1851.733-0.56530.68750.02790.02240.03360.2398-0.03170.0606-0.0404-0.12570.00380.095-0.01810.03870.0406-0.01340.16071.26626.30720.934
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 64
2X-RAY DIFFRACTION2A65 - 169
3X-RAY DIFFRACTION3A170 - 248
4X-RAY DIFFRACTION4B2 - 78
5X-RAY DIFFRACTION5B79 - 169
6X-RAY DIFFRACTION6B170 - 248

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