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- PDB-4z0t: Crystal Structure of a putative oxoacyl-(acyl carrier protein) re... -

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Basic information

Entry
Database: PDB / ID: 4z0t
TitleCrystal Structure of a putative oxoacyl-(acyl carrier protein) reductase from Brucella ovis
ComponentsOxidoreductase, short-chain dehydrogenase/reductase family
KeywordsOXIDOREDUCTASE / short-chain dehydrogenase/reductase family / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
BROMIDE ION / Oxidoreductase, short-chain dehydrogenase/reductase family / Oxidoreductase, short-chain dehydrogenase/reductase family
Similarity search - Component
Biological speciesBrucella ovis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a putative oxoacyl-(acyl carrier protein) reductase from Brucella ovis.
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Oxidoreductase, short-chain dehydrogenase/reductase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1847
Polymers27,7401
Non-polymers4446
Water4,017223
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.210, 80.210, 145.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Oxidoreductase, short-chain dehydrogenase/reductase family


Mass: 27740.135 Da / Num. of mol.: 1 / Fragment: UNP residues 10-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella ovis (bacteria) / Strain: ATCC 25840 / 63/290 / NCTC 10512 / Gene: BOV_0452 / Plasmid: BrovA.01365.c.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5VP18, UniProt: A0A0M3KL28*PLUS
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.11 Å3/Da / Density % sol: 41.59 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: BrovA.01365.c.B1.PS02315 at 20.8mg/ml mixed 1:1 with Morpheus(B6): 10% PEG-8000, 20% ethylene glycol, 0.1 M MOPS/ HEPES-Na, pH 7.5, 0.03 M each sodium fluoride, sodium bromide, sodium iodide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 12, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 38065 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5.7 % / Biso Wilson estimate: 16.44 Å2 / Rmerge F obs: 0.997 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.073 / Χ2: 0.962 / Net I/σ(I): 14.66 / Num. measured all: 216173
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.5-1.545.70.8540.4843.3815884280628040.53499.9
1.54-1.580.8990.3974.1415243269926970.43899.9
1.58-1.630.9290.3244.9514980264226420.357100
1.63-1.680.950.269614753258825870.297100
1.68-1.730.9660.2246.9914053247624750.247100
1.73-1.790.9740.1898.2213728240424040.209100
1.79-1.860.9830.14610.4313347233823380.16100
1.86-1.940.9890.11512.8812870225622550.127100
1.94-2.020.9920.09615.2512366217321710.10699.9
2.02-2.120.9940.08117.6311794206320610.08999.9
2.12-2.240.9950.0720.3611236197519650.07799.5
2.24-2.370.9950.06522.0310670187918700.07299.5
2.37-2.540.9950.06123.4110001175517440.06799.4
2.54-2.740.9950.05925.069352165316380.06599.1
2.74-30.9960.05326.738610153015140.05899
3-3.350.9950.05228.457831139513760.05798.6
3.35-3.870.9960.0529.846868123512120.05698.1
3.87-4.740.9960.04930.85838106410400.05597.7
4.74-6.710.9960.04930.2144628408130.05596.8
6.710.9940.05128.9622875084590.05890.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation4.21 Å41.46 Å
Translation4.21 Å41.46 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.5.7phasing
PHENIX(phenix.refine: dev_1932)refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
ARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3F5Q

3f5q


Resolution: 1.5→40.105 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1854 1817 4.77 %
Rwork0.1499 36246 -
obs0.1516 38063 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 64.72 Å2 / Biso mean: 24.8389 Å2 / Biso min: 9.27 Å2
Refinement stepCycle: final / Resolution: 1.5→40.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1850 0 12 224 2086
Biso mean--50.81 34.82 -
Num. residues----244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061948
X-RAY DIFFRACTIONf_angle_d0.9882648
X-RAY DIFFRACTIONf_chiral_restr0.044312
X-RAY DIFFRACTIONf_plane_restr0.004338
X-RAY DIFFRACTIONf_dihedral_angle_d10.777747
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.54060.20641390.157727582897100
1.5406-1.58590.23371500.155627432893100
1.5859-1.63710.23541250.149127702895100
1.6371-1.69560.20031330.144827792912100
1.6956-1.76350.20061420.146627672909100
1.7635-1.84380.1841350.139627712906100
1.8438-1.9410.19531390.140527682907100
1.941-2.06260.16841530.143427872940100
2.0626-2.22180.19011450.137327682913100
2.2218-2.44540.16881500.14322786293699
2.4454-2.79910.20581310.15712818294999
2.7991-3.52630.16521410.16012824296599
3.5263-40.11930.18441340.15122907304196

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