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- PDB-4ni5: Crystal Structure of a Short Chain Dehydrogenase from Brucella suis -

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Basic information

Entry
Database: PDB / ID: 4ni5
TitleCrystal Structure of a Short Chain Dehydrogenase from Brucella suis
ComponentsOxidoreductase, short-chain dehydrogenase/reductase family protein
KeywordsOXIDOREDUCTASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / short chain dehydrogenase / dehydrogenase
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
Oxidoreductase, short-chain dehydrogenase/reductase family protein
Similarity search - Component
Biological speciesBrucella suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsDranow, D.M. / Abendroth, J. / 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 suis
Authors: Dranow, D.M. / Abendroth, J. / Edwards, T.E. / Lorimer, D.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Sep 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: Oxidoreductase, short-chain dehydrogenase/reductase family protein
B: Oxidoreductase, short-chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0863
Polymers54,0612
Non-polymers241
Water7,098394
1
A: Oxidoreductase, short-chain dehydrogenase/reductase family protein
B: Oxidoreductase, short-chain dehydrogenase/reductase family protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)108,1716
Polymers108,1234
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area12490 Å2
ΔGint-76 kcal/mol
Surface area28630 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2700 Å2
ΔGint-23 kcal/mol
Surface area17860 Å2
MethodPISA
3
A: Oxidoreductase, short-chain dehydrogenase/reductase family protein
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)54,1104
Polymers54,0612
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3180 Å2
ΔGint-15 kcal/mol
Surface area17310 Å2
MethodPISA
4
B: Oxidoreductase, short-chain dehydrogenase/reductase family protein

B: Oxidoreductase, short-chain dehydrogenase/reductase family protein


Theoretical massNumber of molelcules
Total (without water)54,0612
Polymers54,0612
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3170 Å2
ΔGint-15 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.440, 130.390, 114.120
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-430-

HOH

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Components

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


Mass: 27030.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella suis (bacteria) / Strain: ATCC 23445 / NCTC 10510 / Gene: BSUIS_A1171 / Production host: Escherichia coli (E. coli) / References: UniProt: B0CGS2
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / 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: 2.15 Å3/Da / Density % sol: 42.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: JCSG(d2): 30% PEG 400, 200mM MgCl2, 0.1M HEPES/NaOH pH 7.5, 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 24, 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: 1.7→50 Å / Num. all: 51576 / Num. obs: 51407 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 21.808 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 19.04
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.740.473.717555365996.9
1.74-1.790.4044.9721675366199.9
1.79-1.840.3196.221673360999.9
1.84-1.90.2657.5721053348699.9
1.9-1.960.2169.0320191335399.9
1.96-2.030.16911.3519524323399.9
2.03-2.110.14313.1190903178100
2.11-2.190.11116.1718220303599.9
2.19-2.290.10117.6917451290999.9
2.29-2.40.08420.6116776280699.9
2.4-2.530.07722.0715666262699.9
2.53-2.690.06624.78151312553100
2.69-2.870.05628.0613948236899.9
2.87-3.10.04732.79128522210100
3.1-3.40.04236.1811664204499.9
3.4-3.80.03641.310428186599.8
3.8-4.390.03344.99018165499.9
4.39-5.380.0346.997806140199.6
5.38-7.60.03143.476262111899.9
7.60.02649.44320063997.9

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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 3VTZ

3vtz


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.1704 / WRfactor Rwork: 0.1405 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8926 / SU B: 3.366 / SU ML: 0.055 / SU R Cruickshank DPI: 0.0869 / SU Rfree: 0.0868 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.087 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1807 2611 5.1 %RANDOM
Rwork0.1506 ---
all0.1521 54018 --
obs0.1521 51407 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 51.27 Å2 / Biso mean: 16.709 Å2 / Biso min: 3.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0 Å20 Å2
2--0.34 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3287 0 1 394 3682
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193410
X-RAY DIFFRACTIONr_bond_other_d0.0010.023314
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9534644
X-RAY DIFFRACTIONr_angle_other_deg0.83337575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4735469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64824.468141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.67915540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7451521
X-RAY DIFFRACTIONr_chiral_restr0.0970.2553
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023991
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02762
X-RAY DIFFRACTIONr_mcbond_it0.7610.7991821
X-RAY DIFFRACTIONr_mcbond_other0.7620.7991820
X-RAY DIFFRACTIONr_mcangle_it1.2751.1882273
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 179 -
Rwork0.207 3476 -
all-3655 -
obs--96.85 %
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)
15.3153-0.3673-0.12873.662-0.88891.81860.0246-0.3188-0.00540.355-0.061-0.1055-0.06220.11390.03640.0624-0.0237-0.01950.0595-0.01770.03419.760122.476546.9868
23.2191-0.29650.9572.0657-0.60063.2925-0.076-0.03170.26210.23390.01070.0334-0.1525-0.10580.06530.0968-0.0157-0.00880.0213-0.03930.152413.888436.020940.0459
35.6571.790.18763.6338-1.3591.84-0.0146-0.11210.36880.1874-0.0313-0.0087-0.11590.01150.04590.0381-0.014-0.00760.0415-0.03470.056820.563628.522839.5956
46.04330.61890.70964.0794-0.30861.63460.0587-0.37470.36560.2244-0.06580.087-0.1425-0.06940.00710.04420.02250.01080.0662-0.04190.0646-9.367131.068436.1878
51.04580.1491-0.07030.2442-0.2230.2271-0.0222-0.0310.0870.02950.0073-0.027-0.03080.00260.01490.0376-0.00120.010.0571-0.01560.05627.717321.331634.2129
61.11470.0397-0.28320.32360.09660.8361-0.018-0.0575-0.02930.0512-0.0037-0.0193-0.00080.04380.02170.05270.00040.00090.03860.00410.02857.306310.718342.9446
71.44660.88170.0052.8-0.17164.59870.0196-0.0789-0.0973-0.0097-0.1052-0.2947-0.05150.32270.08570.02990.0353-0.00990.09350.02350.076320.8743-6.497343.9932
83.28882.24962.21826.08993.34384.42260.08980.0082-0.3721-0.12190.0677-0.54870.20580.3339-0.15750.06940.05830.01480.07160.02440.092920.6973-14.613142.3732
94.28761.13684.851.35552.38889.720.1129-0.1334-0.21580.06330.0285-0.0830.27940.0304-0.14150.0970.0301-0.00010.02240.01810.07311.3604-20.068946.0866
100.89240.15031.58390.16230.17464.30580.00240.1-0.0657-0.01840.0172-0.03840.1570.3457-0.01960.06790.03660.01470.048-0.00420.033510.4214-11.245930.7456
110.24490.0324-0.00460.2605-0.09740.89530.0270.0058-0.03650.00130.0106-0.03350.09880.0553-0.03760.06070.01510.00520.0526-0.00450.03586.783-6.607634.2925
120.8953-0.0811-0.20110.2537-0.14291.43560.0108-0.0168-0.01750.00280.0068-0.0754-0.00590.105-0.01760.03190.00420.00740.0419-0.00690.05815.6154.919732.9521
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 35
2X-RAY DIFFRACTION2A36 - 73
3X-RAY DIFFRACTION3A74 - 91
4X-RAY DIFFRACTION4A92 - 107
5X-RAY DIFFRACTION5A108 - 201
6X-RAY DIFFRACTION6A202 - 246
7X-RAY DIFFRACTION7B1 - 26
8X-RAY DIFFRACTION8B27 - 61
9X-RAY DIFFRACTION9B62 - 79
10X-RAY DIFFRACTION10B80 - 101
11X-RAY DIFFRACTION11B102 - 200
12X-RAY DIFFRACTION12B201 - 246

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