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- PDB-5idq: Crystal structure of a Short-chain dehydrogenase/reductase (SDR)f... -

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Basic information

Entry
Database: PDB / ID: 5idq
TitleCrystal structure of a Short-chain dehydrogenase/reductase (SDR)from Burkholderia vietnamiensis at 1.55 A resolution
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / SSGCID / Short-chain dehydrogenase/reductase SDR / Burkholderia vietnamiensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyshort chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / nucleotide binding / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Short-chain dehydrogenase/reductase SDR
Function and homology information
Biological speciesBurkholderia vietnamiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a Short-chain dehydrogenase/reductase (SDR)from Burkholderia vietnamiensis at 1.55 A resolution
Authors: Yano, J.K. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)50,0852
Polymers50,0852
Non-polymers00
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-32 kcal/mol
Surface area16350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.370, 49.270, 66.820
Angle α, β, γ (deg.)90.000, 94.710, 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.rB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4JIB1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.02 Å3/Da / Density % sol: 39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MCSG1 condition D10: 40% PEG 3350,0.2 M Calcium Acentate, 0.1 M Sodium Cacodylate pH 6.5, BuviA.00010.rB1 at 20.9 mg/ml, 1:1 drop to protein ratio. Direct cryo, plate 269027d10, puck ktx5 position 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.55→47.01 Å / Num. obs: 57605 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 4.53 % / Biso Wilson estimate: 13.82 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.09
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.55-1.590.5292.97199.2
1.59-1.630.4483.48199.1
1.63-1.680.3943.93199.1
1.68-1.730.3164.83199.1
1.73-1.790.2555.89199.1
1.79-1.850.2087.25199.4
1.85-1.920.1748.43199.5
1.92-20.13110.97199.8
2-2.090.10413.17199.1
2.09-2.190.08615.5199.6
2.19-2.310.07817.14199.6
2.31-2.450.06319.55199.8
2.45-2.620.06120.53199.6
2.62-2.830.05622.55199.8
2.83-3.10.04825.07199.7
3.1-3.470.04427.28199.7
3.47-40.0429.03199.6
4-4.90.03729.8199.7
4.9-6.930.0428.87199.8
6.93-47.010.03728.82194.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXdev_2289refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SNY

1sny


Resolution: 1.55→47.01 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.21
RfactorNum. reflection% reflection
Rfree0.2063 1936 3.36 %
Rwork0.1731 --
obs0.1742 57585 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 96.69 Å2 / Biso mean: 22.033 Å2 / Biso min: 6.21 Å2
Refinement stepCycle: final / Resolution: 1.55→47.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3191 0 0 403 3594
Biso mean---31.48 -
Num. residues----434
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113314
X-RAY DIFFRACTIONf_angle_d1.174530
X-RAY DIFFRACTIONf_chiral_restr0.069532
X-RAY DIFFRACTIONf_plane_restr0.008592
X-RAY DIFFRACTIONf_dihedral_angle_d12.7931980
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 (%)
1.5501-1.58890.28961390.23363974411399
1.5889-1.63180.23781130.2233933404699
1.6318-1.67980.25721340.21753939407399
1.6798-1.73410.24111650.19993909407499
1.7341-1.7960.22891500.19123920407099
1.796-1.8680.22041530.18513944409799
1.868-1.9530.22161520.181139414093100
1.953-2.05590.24391090.17144011412099
2.0559-2.18470.19881170.1733991410899
2.1847-2.35340.19141640.166339604124100
2.3534-2.59020.18481300.161840114141100
2.5902-2.9650.21251410.1739914132100
2.965-3.73540.17981300.160540354165100
3.7354-47.03160.19171390.15934090422999
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)
13.39891.4426-1.16531.6019-0.46763.1579-0.04240.17360.0332-0.21270.04950.19640.0987-0.3434-0.01810.1243-0.0299-0.04570.1497-0.02530.117765.2981-0.090558.0623
20.8629-0.0586-0.02651.23170.7942.2260.0202-0.0027-0.0223-0.0884-0.04880.121-0.0814-0.24590.02090.08210.0093-0.01320.12090.01310.088869.45766.686374.1157
31.3470.4442-0.47851.2360.5962.7448-0.02220.0389-0.0112-0.06550.0663-0.0518-0.08340.1543-0.06840.0679-0.0059-0.00030.0778-0.00640.079181.32765.286666.2074
42.8658-1.57791.12362.442-0.24914.0745-0.024-0.1917-0.10010.17730.04450.1093-0.2498-0.38750.00710.1420.01310.0410.1625-0.02380.091366.647616.6472108.2238
51.4833-1.01830.35081.0645-0.5462.21150.003-0.44150.09230.3201-0.09130.405-0.0332-0.8038-0.090.21060.02460.08030.4032-0.04650.221958.497618.5982105.75
62.2248-0.5504-0.22490.7133-0.28381.9152-0.1286-0.08820.31090.13980.05620.3159-0.3439-0.41920.06690.20870.08290.0110.20080.01130.21161.180422.0896.9172
71.18440.28590.05542.24370.78312.15860.0270.00430.03230.0253-0.15770.268-0.0719-0.49850.10790.09520.02220.00420.2162-0.00360.131963.083811.474687.7628
81.65150.70980.11292.79581.27812.77140.02170.0474-0.06740.07830.013-0.02060.15130.0413-0.06750.0688-0.0221-0.00230.07720.02160.057275.40217.980491.1828
91.66110.30570.22941.00070.94022.431-0.02730.0002-0.00460.03640.04570.0476-0.0822-0.05510.00070.0643-0.00390.00530.0698-0.00360.071273.402412.150891.4252
101.7136-0.35440.26062.27330.14382.04990.0361-0.16150.09960.12180.0082-0.0942-0.06940.32940.03910.0822-0.03650.00570.071-0.01540.08479.947414.620999.6872
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 66 )A0 - 66
2X-RAY DIFFRACTION2chain 'A' and (resid 67 through 163 )A67 - 163
3X-RAY DIFFRACTION3chain 'A' and (resid 164 through 225 )A164 - 225
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 23 )B1 - 23
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 55 )B24 - 55
6X-RAY DIFFRACTION6chain 'B' and (resid 56 through 81 )B56 - 81
7X-RAY DIFFRACTION7chain 'B' and (resid 82 through 121 )B82 - 121
8X-RAY DIFFRACTION8chain 'B' and (resid 122 through 143 )B122 - 143
9X-RAY DIFFRACTION9chain 'B' and (resid 144 through 189 )B144 - 189
10X-RAY DIFFRACTION10chain 'B' and (resid 190 through 225 )B190 - 225

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