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- PDB-5el0: Crystal structure of an Oxidoreductase (short chain dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 5el0
TitleCrystal structure of an Oxidoreductase (short chain dehydrogenase/reductase family) from Brucella ovis in complex with a partially ordered NAD
ComponentsOxidoreductase, short chain dehydrogenase/reductase family
KeywordsOXIDOREDUCTASE / SSGCID / Brucella ovis / brucellosis / short chain dehydrogenase/reductase family / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Oxidoreductase, short chain dehydrogenase/reductase family
Similarity search - Component
Biological speciesBrucella ovis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of an Oxidoreductase (short chain dehydrogenase/reductase family) from Brucella ovis in complex with a partially ordered NAD
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionNov 4, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)30,6723
Polymers29,8891
Non-polymers7832
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.350, 99.930, 100.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 29888.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella ovis (strain ATCC 25840 / 63/290 / NCTC 10512) (bacteria)
Strain: ATCC 25840 / 63/290 / NCTC 10512 / Gene: BOV_0113 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3AQ75
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Mycrolytic MCSG1 screen, A10: 28% polypropylene glycol, 200mM CaCl2, 100mM HEPES/NaOH pH 7.5; BrovA.01365.b.B1.PS02128 at 19mg/ml, 3mM NADP; cryo: 15% PEG 400; tray 259821a10; puck hmh25-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 25, 2015
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 23344 / Num. obs: 23244 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Biso Wilson estimate: 23.05 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.045 / Χ2: 0.987 / Net I/σ(I): 33.26 / Num. measured all: 235383
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.85-1.96.010.9020.523.1510204170016990.5799.9
1.9-1.950.9360.3924.3710194164316400.42899.8
1.95-2.010.9670.2746.3310449161816150.29899.8
2.01-2.070.9750.2168.2810464156715660.23499.9
2.07-2.140.9880.17211.1211222154215410.18699.9
2.14-2.210.9930.13416.6812695145314470.14399.6
2.21-2.290.9950.1241913397143514210.13199
2.29-2.390.9970.09823.6613275135213420.10499.3
2.39-2.490.9980.08726.5813516132113050.09198.8
2.49-2.620.9980.07729.9614089128012760.08199.7
2.62-2.760.9990.06834.9914496119611850.07199.1
2.76-2.930.9990.0642.3216147114811380.06299.1
2.93-3.130.9990.04851.9815514108110760.0599.5
3.13-3.380.9990.03862.59141909949910.03999.7
3.38-3.710.0378.24134419359340.03199.9
3.7-4.1410.02787.13119908558480.02899.2
4.14-4.7810.02297.93104927527520.023100
4.78-5.8510.02490.791046516510.025100
5.85-8.2710.02688.7669345125120.027100
8.27-500.9990.019103.8935703093050.0298.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
PHENIXdev_2210refinement
Cootmodel building
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native structure, PDB entry 4X54

4x54


Resolution: 1.85→47.12 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1942 1916 8.24 %Random selection
Rwork0.163 21328 --
obs0.1656 23244 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.77 Å2 / Biso mean: 31.4154 Å2 / Biso min: 10.82 Å2
Refinement stepCycle: final / Resolution: 1.85→47.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 40 157 1819
Biso mean--37.49 38.15 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061726
X-RAY DIFFRACTIONf_angle_d0.8032364
X-RAY DIFFRACTIONf_chiral_restr0.055278
X-RAY DIFFRACTIONf_plane_restr0.005313
X-RAY DIFFRACTIONf_dihedral_angle_d12.5451050
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8501-1.89630.34691630.262614741637100
1.8963-1.94760.27371280.218415071635100
1.9476-2.00490.20991120.17715151627100
2.0049-2.06960.20511400.176415091649100
2.0696-2.14360.21410.168715101651100
2.1436-2.22940.18021400.15881513165399
2.2294-2.33090.18711330.15781496162999
2.3309-2.45380.22191470.15021484163199
2.4538-2.60750.19491410.16051524166599
2.6075-2.80880.18551260.17191524165099
2.8088-3.09140.21931220.16241520164299
3.0914-3.53860.18871470.155915401687100
3.5386-4.45780.16071230.136415871710100
4.4578-47.13530.17771530.170616251778100
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)
13.3932-2.4166-1.09812.54970.53236.4987-0.0291-0.12350.3382-0.0179-0.06110.1329-0.3663-0.33270.12140.18090.02830.02240.1697-0.08310.25712.9793223.0978218.3611
25.7732-0.4359-0.30984.96560.29213.2551-0.07420.18350.5699-0.36870.080.6228-0.568-0.53040.01490.30990.0809-0.01670.23560.01430.233315.179221.1759206.0777
31.95850.03240.15113.63580.62821.6328-0.004-0.37170.20120.23630.05510.133-0.0935-0.0661-0.04750.12120.01880.01840.2015-0.04020.122121.1599209.6397220.0816
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 25 through 57 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 99 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 100 through 263 )A0

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