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- PDB-4npc: Crystal Structure of an Oxidoreductase, Short-Chain Dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 4npc
TitleCrystal Structure of an Oxidoreductase, Short-Chain Dehydrogenase/Reductase Family Protein from Brucella suis
ComponentsSorbitol dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / reductase / short-chain dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
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
ACETATE ION / Sorbitol dehydrogenase
Similarity search - Component
Biological speciesBrucella suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsDranow, D.M. / Davies, D.R. / Edwards, T.E. / Lorimer, D. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal Structure of an Oxidoreductase, Short-Chain Dehydrogenase/Reductase Family Protein from Brucella suis
Authors: Dranow, D.M. / Davies, D.R. / Edwards, T.E. / Lorimer, D.
History
DepositionNov 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 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: Sorbitol dehydrogenase
B: Sorbitol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,1154
Polymers54,9972
Non-polymers1182
Water6,972387
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-24 kcal/mol
Surface area20410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.740, 87.740, 117.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Sorbitol dehydrogenase /


Mass: 27498.475 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: polS, BSUIS_A1688 / Production host: Escherichia coli (E. coli) / References: UniProt: B0CIA7
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MCSG1(f5): 0.2M Sodium Acetate, 20% PEG-3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 30, 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: 1.75→70.19 Å / Num. all: 46707 / Num. obs: 46513 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 29.873 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 29.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.80.4934.0623148339399.9
1.8-1.840.3875.27235633286100
1.84-1.90.2926.923201324299.9
1.9-1.960.2199.15222733120100
1.96-2.020.16911.8821800304299.8
2.02-2.090.13314.8121054296199.9
2.09-2.170.119.1119993280499.8
2.17-2.260.07923.4819626276699.9
2.26-2.360.06428.3418623262599.8
2.36-2.470.05730.81179742541100
2.47-2.610.04836.0416812238699.7
2.61-2.770.04140.6216008228899.7
2.77-2.960.03547.514907214999.5
2.96-3.20.02954.9313799200099.7
3.2-3.50.02562.412729186599.5
3.5-3.910.02369.8411533167899.1
3.91-4.520.02176.0810172149098.7
4.52-5.530.02175.028590129398.7
5.53-7.830.02172.316500101197.5
7.830.0271.42309757392.7

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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 4EGF

4egf


Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / WRfactor Rfree: 0.1799 / WRfactor Rwork: 0.1448 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.887 / SU B: 4.029 / SU ML: 0.066 / SU R Cruickshank DPI: 0.1013 / SU Rfree: 0.1013 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1871 2353 5.1 %RANDOM
Rwork0.1487 ---
obs0.1506 46512 99.58 %-
all-48865 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 55.25 Å2 / Biso mean: 26.4 Å2 / Biso min: 5.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å2-0 Å2-0 Å2
2---0.41 Å2-0 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3614 0 8 387 4009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193747
X-RAY DIFFRACTIONr_bond_other_d0.0010.023712
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9625107
X-RAY DIFFRACTIONr_angle_other_deg0.80938543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0925526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.71225.798119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.81915605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.373156
X-RAY DIFFRACTIONr_chiral_restr0.090.2616
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024337
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02769
X-RAY DIFFRACTIONr_mcbond_it0.9311.3542051
X-RAY DIFFRACTIONr_mcbond_other0.9281.3522048
X-RAY DIFFRACTIONr_mcangle_it1.3912.0232568
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 166 -
Rwork0.203 3224 -
all-3390 -
obs--99.94 %
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)
11.46650.4967-0.21811.23790.00780.395-0.00750.0315-0.1829-0.0566-0.0133-0.2940.02760.03620.02080.03550.04160.03030.08-0.020.147930.8363-4.007224.97
21.2861-0.1873-0.15551.21150.34210.3372-0.0418-0.07620.0337-0.00910.0339-0.19680.01550.07780.0080.08530.02750.00190.1202-0.01180.05516.07026.04927.5678
36.8788-0.957-0.81670.75152.803511.8031-0.1339-1.06650.3585-0.06760.2652-0.0799-0.35870.636-0.13130.3205-0.14330.06770.4379-0.13670.39819.70993.543949.811
41.36370.1846-0.43240.8155-0.16870.88630.046-0.1804-0.07770.0953-0.0402-0.1682-0.04650.0808-0.00590.08090.025-0.02630.09120.00640.040512.6762-6.663736.6681
51.50790.5361-0.17512.40670.08470.75060.04780.08780.36810.08490.05510.1680.00550.0024-0.10290.0343-0.00330.01750.04770.02460.1668-5.198232.080827.4591
61.3486-0.2991-0.52141.13590.21820.5727-0.00730.02050.2203-0.02980.0521-0.0770.04380.0821-0.04480.08240.00680.00210.09990.00120.04354.52217.061425.6793
71.2682-3.5068-1.963812.41422.97095.28780.30480.0717-0.0239-0.8977-0.23820.1628-0.4806-0.0111-0.06660.3722-0.05940.05130.28990.03550.2662-3.760616.22624.6396
81.58960.44710.30671.7020.38920.2541-0.07020.24550.1516-0.19040.090.1012-0.02390.1076-0.01980.13-0.0097-0.01410.14770.03190.0558-9.683812.12120.6131
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 96
2X-RAY DIFFRACTION2A97 - 199
3X-RAY DIFFRACTION3A200 - 209
4X-RAY DIFFRACTION4A210 - 257
5X-RAY DIFFRACTION5B5 - 98
6X-RAY DIFFRACTION6B99 - 199
7X-RAY DIFFRACTION7B200 - 208
8X-RAY DIFFRACTION8B209 - 257

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