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- PDB-4nim: Crystal Structure of a Short Chain Dehydrogenase from Brucella me... -

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Basic information

Entry
Database: PDB / ID: 4nim
TitleCrystal Structure of a Short Chain Dehydrogenase from Brucella melitensis
ComponentsVersicolorin reductase
KeywordsOXIDOREDUCTASE / reductase / short chain dehydrogenases / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
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
Versicolorin reductase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsDranow, D.M. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of a Short Chain Dehydrogenase from Brucella melitensis
Authors: Dranow, D.M. / Edwards, T.E. / Lorimer, D.
History
DepositionNov 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Structure summary
Revision 1.2Sep 16, 2015Group: Other / Structure summary
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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

Downloads & links

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Assembly

Deposited unit
A: Versicolorin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1143
Polymers29,9901
Non-polymers1242
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Versicolorin reductase
hetero molecules

A: Versicolorin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2286
Polymers59,9802
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
Buried area4660 Å2
ΔGint-22 kcal/mol
Surface area19170 Å2
MethodPISA
3
A: Versicolorin reductase
hetero molecules

A: Versicolorin reductase
hetero molecules

A: Versicolorin reductase
hetero molecules

A: Versicolorin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,45712
Polymers119,9604
Non-polymers4978
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area18610 Å2
ΔGint-104 kcal/mol
Surface area29050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.210, 118.210, 85.180
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-444-

HOH

21A-452-

HOH

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Components

#1: Protein Versicolorin reductase


Mass: 29990.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: ATCC 23457 / Gene: BMEA_A1386 / References: UniProt: C0RJU5
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.48 Å3/Da / Density % sol: 50.41 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: JCSG+(d3): 50% PEG-200, 100mM Sodium phosphate dibasic/ potassium phosphate monobasic, pH 6.2, 200mM NaCl, 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: 0.97857 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 16, 2013 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 28196 / Num. obs: 27974 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.3 % / Biso Wilson estimate: 27.611 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 27.64
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.850.4874.9519456204799.7
1.85-1.90.3936.0918706197099.6
1.9-1.950.3217.4318625196799.8
1.95-2.010.2429.5917700187899.9
2.01-2.080.19911.6417433184699.7
2.08-2.150.1611416751177199.6
2.15-2.230.12417.7416172172599.8
2.23-2.320.10520.5415231162799.4
2.32-2.430.08923.6614959160399.8
2.43-2.550.08325.4814122151199.3
2.55-2.680.06829.7313543145299.3
2.68-2.850.05734.2912730136598.8
2.85-3.040.04741.711888129198.9
3.04-3.290.03948.2310881118998.9
3.29-3.60.03257.979879110998.6
3.6-4.020.02767.459093100898.5
4.02-4.650.02475.61832689998
4.65-5.690.02474.98700475997.3
5.69-8.050.02374.24547360497.1
8.050.0281.23285135394.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.5phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YBV

1ybv


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1655 / WRfactor Rwork: 0.1375 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8538 / SU B: 4.906 / SU ML: 0.074 / SU R Cruickshank DPI: 0.092 / SU Rfree: 0.0933 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1864 1409 5 %RANDOM
Rwork0.1542 ---
all0.1558 29383 --
obs0.1558 27974 99.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.78 Å2 / Biso mean: 25.359 Å2 / Biso min: 6.23 Å2
Baniso -1Baniso -2Baniso -3
1--1.47 Å20 Å2-0 Å2
2---1.47 Å20 Å2
3---2.93 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 0 8 167 1938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191831
X-RAY DIFFRACTIONr_bond_other_d0.0010.021785
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.9632482
X-RAY DIFFRACTIONr_angle_other_deg0.82634063
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4355248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.45522.72777
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80815290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5961519
X-RAY DIFFRACTIONr_chiral_restr0.0940.2287
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022142
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02435
X-RAY DIFFRACTIONr_mcbond_it0.9651.286971
X-RAY DIFFRACTIONr_mcbond_other0.9651.286970
X-RAY DIFFRACTIONr_mcangle_it1.5521.9211214
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 90 -
Rwork0.246 1957 -
all-2047 -
obs--99.76 %
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)
12.28720.2837-0.46052.71140.62182.958-0.03330.1538-0.0884-0.31-0.0104-0.09840.09850.21730.04370.22230.01520.06020.07550.01410.024674.120810.9927-5.6642
20.4253-0.15340.25930.8502-0.28960.81090.0250.04860.0009-0.1822-0.0118-0.0338-0.08510.1466-0.01320.12620.00380.00790.06740.00490.057671.19714.54699.0894
33.1449-2.3506-0.60665.0356-0.09492.9419-0.02830.0638-0.1092-0.25340.0084-0.1320.16670.24480.01990.1548-0.01930.02210.0778-0.00310.103668.15882.19114.107
40.24940.03090.08840.7706-0.16861.10640.01290.0269-0.0526-0.17170.0168-0.0390.05350.0585-0.02970.11390.01760.00970.0634-0.00880.0965.3043-2.873912.2078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 52
2X-RAY DIFFRACTION2A53 - 179
3X-RAY DIFFRACTION3A180 - 231
4X-RAY DIFFRACTION4A232 - 269

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