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- PDB-5idw: Crystal structure of an oxidoreductase from Burkholderia vietnami... -

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Basic information

Entry
Database: PDB / ID: 5idw
TitleCrystal structure of an oxidoreductase from Burkholderia vietnamiensis in complex with NADP
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / SSGCID / short chain dehydrogenase/reductase family / NADP / Brucella ovis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


short chain dehydrogenase / 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 / Short-chain dehydrogenase/reductase SDR
Similarity search - Component
Biological speciesBurkholderia vietnamiensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of an oxidoreductase from Burkholderia vietnamiensis in complex with NADP
Authors: Mayclin, S.J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: 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_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5724
Polymers50,0852
Non-polymers1,4872
Water6,756375
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-40 kcal/mol
Surface area15920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.810, 49.230, 66.960
Angle α, β, γ (deg.)90.000, 94.990, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 25042.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria)
Strain: G4 / LMG 22486 / Gene: Bcep1808_3023 / Plasmid: BuviA.00010.r.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4JIB1
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / 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: 2.03 Å3/Da / Density % sol: 39 % / Mosaicity: 0.23 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: MCSG1 D10 (269027d10): 0.2 M Calcium Acetate 0.1 M Sodium Cacodylate:HCl pH 6.5 40% (v/v ) PEG 300; protein conc. 20.9mg/mL; 5mM NADP soak; direct cryo; puck foe9-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 19, 2016 / Details: RIGAKU VARIMAX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 27131 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.23 % / Biso Wilson estimate: 15.72 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.59
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.052.130.3462.63197.1
2.05-2.110.3143.11196.5
2.11-2.170.2793.86199
2.17-2.240.2654.34198.6
2.24-2.310.264.58198.7
2.31-2.390.1946.05199.4
2.39-2.480.2246.08199.5
2.48-2.580.2116.36199.6
2.58-2.70.1856.88199.9
2.7-2.830.1637.44199.5
2.83-2.980.1268.96199.7
2.98-3.160.10610.36199.9
3.16-3.380.0813.08199.8
3.38-3.650.06915.96199.8
3.65-40.06118.85199.4
4-4.470.05819.85199.1
4.47-5.160.05619.03199.5
5.16-6.320.07714.161100
6.32-8.940.06516.6198.8
8.940.04224.8195.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2313refinement
PDB_EXTRACT3.2data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IDQ

5idq


Resolution: 2→50 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.13
RfactorNum. reflection% reflection
Rfree0.237 1703 6.28 %
Rwork0.1813 --
obs0.1849 27115 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.5 Å2 / Biso mean: 20.1734 Å2 / Biso min: 5.55 Å2
Refinement stepCycle: final / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 96 377 3770
Biso mean--19.77 29.25 -
Num. residues----450
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073487
X-RAY DIFFRACTIONf_angle_d0.8254772
X-RAY DIFFRACTIONf_chiral_restr0.05554
X-RAY DIFFRACTIONf_plane_restr0.005617
X-RAY DIFFRACTIONf_dihedral_angle_d14.9652034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.05890.33471180.23672090220897
2.0589-2.12530.29331250.22192082220797
2.1253-2.20130.28621320.19242095222799
2.2013-2.28940.25661390.18992091223098
2.2894-2.39360.25321430.17422110225399
2.3936-2.51980.25681430.18121002243100
2.5198-2.67760.24111590.195521152274100
2.6776-2.88430.27851170.193921532270100
2.8843-3.17450.24231400.186521392279100
3.1745-3.63370.22481640.170421292293100
3.6337-4.57730.191750.14652111228699
4.5773-43.41510.20341480.17492197234599
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)
12.23090.5139-0.71251.0267-0.1022.478-0.0150.1823-0.1987-0.2692-0.04950.1870.0113-0.27550.06120.1548-0.0234-0.06420.1427-0.02770.131265.23590.290258.165
21.3447-0.3984-0.32091.00750.65462.022-0.0040.0587-0.0027-0.0861-0.03560.0757-0.0437-0.11490.02720.07280.0013-0.01060.09610.01760.079870.98537.256472.2681
30.77540.2295-0.18091.4540.24090.7385-0.03070.0839-0.0824-0.13980.0499-0.05160.10460.2947-0.01670.09380.0310.01190.1093-0.01170.074783.09534.298766.2423
41.9708-0.07610.67231.1213-0.25361.9047-0.0528-0.23320.15010.4004-0.03750.3637-0.0921-0.42290.06090.18580.04790.10310.2042-0.00520.188161.313617.8049105.0838
51.11810.43010.07142.78420.86412.4038-0.01450.00430.070.12640.02020.1462-0.0509-0.1380.00470.05960.01140.00630.10390.01430.066768.141912.036989.8219
62.0647-0.23510.18730.84450.27951.8078-0.0508-0.174-0.06190.17570.0765-0.00660.10410.0128-0.01310.1298-0.01090.01860.08010.00770.055977.206511.758799.7851
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 66 )A1 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 189 )A67 - 189
3X-RAY DIFFRACTION3chain 'A' and (resid 190 through 225 )A190 - 225
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 65 )B1 - 65
5X-RAY DIFFRACTION5chain 'B' and (resid 66 through 163 )B66 - 163
6X-RAY DIFFRACTION6chain 'B' and (resid 164 through 225 )B164 - 225

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