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- PDB-4lvu: Crystal Structure of a Putative Short Chain Dehydrogenase from Bu... -

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Basic information

Entry
Database: PDB / ID: 4lvu
TitleCrystal Structure of a Putative Short Chain Dehydrogenase from Burkholderia thailandensis
ComponentsOxidoreductase, short chain dehydrogenase/reductase family
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
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
Oxidoreductase, short chain dehydrogenase/reductase family
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of a Putative Short Chain Dehydrogenase from Burkholderia thailandensis
Authors: Dranow, D.M. / Edwards, T.E. / Lorimer, D.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,6064
Polymers59,4822
Non-polymers1242
Water12,088671
1
A: Oxidoreductase, short chain dehydrogenase/reductase family
B: Oxidoreductase, short chain dehydrogenase/reductase family
hetero molecules

A: Oxidoreductase, short chain dehydrogenase/reductase family
B: Oxidoreductase, short chain dehydrogenase/reductase family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,2128
Polymers118,9634
Non-polymers2484
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_785-x+2,-y+3,z1
Buried area14620 Å2
ΔGint-64 kcal/mol
Surface area33710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.460, 103.390, 71.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 29740.822 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_I1182 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2SZC0, Oxidoreductases
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 671 / 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: 2.21 Å3/Da / Density % sol: 44.44 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: JCSG+(a5): 20% PEG3350, 200 mM magnesium formate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 19, 2013 / Details: beryllium lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.25→50 Å / Num. all: 146259 / Num. obs: 143334 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.8 % / Biso Wilson estimate: 14.702 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 26.37
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.25-1.280.4564.07692721007894.6
1.28-1.320.395.06749981008696.6
1.32-1.360.345.8373061981696.7
1.36-1.40.2916.7571500962297.1
1.4-1.440.2467.9769257931197.4
1.44-1.490.19110.1266991905397.6
1.49-1.550.15412.3564773877397.8
1.55-1.610.12615.0162193844198.3
1.61-1.690.10717.2359898814498.5
1.69-1.770.09421.3966640781498.6
1.77-1.860.09429.24108636747398.9
1.86-1.980.07236.22104670711999.1
1.98-2.110.05644.6797513665699.2
2.11-2.280.04652.4991656626299.6
2.28-2.50.04158.8685006578799.6
2.5-2.80.03764.2877635527899.8
2.8-3.230.03272.14689324688100
3.23-3.950.02881.84578773982100
3.95-5.590.02785.15447933131100
5.590.02679.3623932182098.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.86 Å
Translation2.5 Å19.86 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JRO

4jro


Resolution: 1.25→45.4 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / WRfactor Rfree: 0.1361 / WRfactor Rwork: 0.1137 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9382 / SU B: 0.922 / SU ML: 0.019 / SU R Cruickshank DPI: 0.0325 / SU Rfree: 0.0329 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.033 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.141 7172 5 %RANDOM
Rwork0.1168 ---
all0.1181 143334 --
obs0.1181 143283 98.05 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.42 Å2 / Biso mean: 13.3299 Å2 / Biso min: 3.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.25→45.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3697 0 8 671 4376
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193930
X-RAY DIFFRACTIONr_bond_other_d0.0010.023858
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9485368
X-RAY DIFFRACTIONr_angle_other_deg0.78538769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3375543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42122.398171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85815598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2221544
X-RAY DIFFRACTIONr_chiral_restr0.0880.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024646
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02954
X-RAY DIFFRACTIONr_mcbond_it1.1170.8992068
X-RAY DIFFRACTIONr_mcbond_other1.1110.8992067
X-RAY DIFFRACTIONr_mcangle_it1.4081.3572593
X-RAY DIFFRACTIONr_rigid_bond_restr1.57837788
X-RAY DIFFRACTIONr_sphericity_free40.9185146
X-RAY DIFFRACTIONr_sphericity_bonded9.67558233
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.203 471 -
Rwork0.187 9602 -
all-10073 -
obs--94.56 %

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