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- PDB-3op4: Crystal structure of putative 3-ketoacyl-(acyl-carrier-protein) r... -

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Basic information

Entry
Database: PDB / ID: 3op4
TitleCrystal structure of putative 3-ketoacyl-(acyl-carrier-protein) reductase from Vibrio cholerae O1 biovar eltor str. N16961 in complex with NADP+
Components3-oxoacyl-[acyl-carrier protein] reductase
KeywordsOXIDOREDUCTASE / 3-ketoacyl-(acyl-carrier-protein) reductase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Rossmann fold / bacterial cell
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ACETATE ION / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Function and homology information
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsHou, J. / Chruszcz, M. / Onopriyenko, O. / Grimshaw, S. / Porebski, P. / Zheng, H. / Savchenko, A. / 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
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: 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 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)54,9966
Polymers53,3912
Non-polymers1,6054
Water9,062503
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)109,99212
Polymers106,7824
Non-polymers3,2108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area20340 Å2
ΔGint-119 kcal/mol
Surface area31900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.058, 104.095, 126.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-320-

HOH

21A-552-

HOH

31B-331-

HOH

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Components

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


Mass: 26695.490 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(DE3)-RIPL
References: UniProt: C3NP04, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: 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
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2M NH4 Sulfate,0.1M Tris, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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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: Jul 9, 2010 / Details: Mirror
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: 1.6→50 Å / Num. all: 61433 / Num. obs: 61433 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 15.4 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 28.9
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.616 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3009 / Rsym value: 0.616 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
REFMAC5.5.0109refinement
Cootmodel building
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.373 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1751 3106 5.1 %RANDOM
Rwork0.14733 ---
all0.14872 58281 --
obs0.14872 58281 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.407 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2--0.13 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3615 0 104 503 4222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0223891
X-RAY DIFFRACTIONr_bond_other_d0.0010.022561
X-RAY DIFFRACTIONr_angle_refined_deg1.8182.0015287
X-RAY DIFFRACTIONr_angle_other_deg1.01536298
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8255526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63724.8150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80815686
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7831527
X-RAY DIFFRACTIONr_chiral_restr0.1050.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024386
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02719
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_it1.0751.52499
X-RAY DIFFRACTIONr_mcbond_other0.3351.51055
X-RAY DIFFRACTIONr_mcangle_it1.86823991
X-RAY DIFFRACTIONr_scbond_it3.65531392
X-RAY DIFFRACTIONr_scangle_it5.3974.51285
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.602→1.644 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 209 -
Rwork0.2 4055 -
obs--95.18 %
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)
10.02880.01390.02950.24680.08460.2455-0.0005-0.009-0.00640.0377-0.0015-0.0076-0.0157-0.02940.0020.06460.0066-0.00330.0286-0.00150.002320.2237.8322.536
20.21870.00970.05590.1404-0.00020.13280.0039-0.0092-0.02330.0217-0.0066-0.0271-0.01670.00290.00270.05740.001-0.00550.03390.00370.007929.7410.7069.283
30.1119-0.0394-0.0520.42260.09110.05110.02260.00820.0169-0.0254-0.0129-0.0171-0.015-0.0165-0.00970.05760.0077-0.00580.02520.00620.006619.27921.233-10.742
40.30470.08320.04040.4907-0.1470.05930.0067-0.00390.0070.01960.02020.0837-0.0076-0.0045-0.02690.05330.00670.00220.0330.0030.01469.74214.0181.047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 192
2X-RAY DIFFRACTION2A193 - 248
3X-RAY DIFFRACTION3B1 - 192
4X-RAY DIFFRACTION4B193 - 248

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