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- PDB-3nyw: Crystal Structure of a betaketoacyl-[ACP] reductase (FabG) from B... -

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Basic information

Entry
Database: PDB / ID: 3nyw
TitleCrystal Structure of a betaketoacyl-[ACP] reductase (FabG) from Bacteroides thetaiotaomicron
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / fatty acid synthesis / 3-oxoacyl-[ACP] reductase / NADP+ binding / Rossmann fold / PSI-II / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / oxidation reduction / Mitochondria
Function / homologyshort chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Putative oxidoreductase
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.16 Å
AuthorsSatyanarayana, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of a betaketoacyl-[ACP] reductase (FabG) from Bacteroides thetaiotaomicron
Authors: Satyanarayana, L. / Burley, S.K. / Swaminathan, S.
History
DepositionJul 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative oxidoreductase
B: Putative oxidoreductase
C: Putative oxidoreductase
D: Putative oxidoreductase


Theoretical massNumber of molelcules
Total (without water)112,0924
Polymers112,0924
Non-polymers00
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9380 Å2
ΔGint-74 kcal/mol
Surface area37760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.883, 105.715, 78.830
Angle α, β, γ (deg.)90.00, 98.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative oxidoreductase


Mass: 28023.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_2380 / Plasmid: pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Codon + RIL / References: UniProt: Q8A562
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 2.2 Å3/Da / Density % sol: 44.16 %
Crystal growTemperature: 298 K / pH: 7
Details: 0.15M DL-Malic acid pH 7.0, 15% w/v PEG 3,350, 10% w/v 1,6,Hexanediol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2010 / 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: 2.16→50 Å / Num. obs: 51961 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 21.9 Å2 / Rsym value: 0.05 / Net I/σ(I): 24.2
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 21.7 / Rsym value: 0.164 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXCDphasing
SHARPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.16→45.83 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.263 4429 -RANDOM
Rwork0.236 ---
obs0.236 51961 92.8 %-
all-51961 --
Displacement parametersBiso mean: 44.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.772 Å20 Å23.292 Å2
2--2.782 Å20 Å2
3----4.554 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.16→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6874 0 0 269 7143
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4211.5
X-RAY DIFFRACTIONc_mcangle_it2.3242
X-RAY DIFFRACTIONc_scbond_it2.4322
X-RAY DIFFRACTIONc_scangle_it3.6252.5
LS refinement shellResolution: 2.16→2.22 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.325 664 -
Rwork0.318 --
obs--83.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1ion.param
X-RAY DIFFRACTION2protein_rep.param
X-RAY DIFFRACTION3water_rep.param

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