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- PDB-5vps: Crystal structure of an SDR from Burkholderia ambifaria in comple... -

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Basic information

Entry
Database: PDB / ID: 5vps
TitleCrystal structure of an SDR from Burkholderia ambifaria in complex with NADPH with a TCEP adduct
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / SGCID / short chain / dehydrogenase / reductase / NADP / NADPH / TCEP / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


: / 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
Chem-9G1 / Short-chain dehydrogenase/reductase SDR
Similarity search - Component
Biological speciesBurkholderia ambifaria (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Biochemistry / Year: 2020
Title: Cautionary Tale of Using Tris(alkyl)phosphine Reducing Agents with NAD+-Dependent Enzymes.
Authors: Patel, S.M. / Smith, T.G. / Morton, M. / Stiers, K.M. / Seravalli, J. / Mayclin, S.J. / Edwards, T.E. / Tanner, J.J. / Becker, D.F.
History
DepositionMay 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7674
Polymers27,6441
Non-polymers1,1233
Water6,449358
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.090, 64.090, 119.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-646-

HOH

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 27644.436 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria (strain MC40-6) (bacteria)
Strain: MC40-6 / Gene: BamMC406_2208 / Plasmid: BuamA.00010.o.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1YU47
#2: Chemical ChemComp-9G1 / [(4~{S})-3-aminocarbonyl-1-[(2~{R},3~{R},4~{S},5~{R})-5-[[[[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-phosphonooxy-oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxymethyl]-3,4-bis(oxidanyl)oxolan-2-yl]piperidin-4-yl]-tris(3-hydroxy-3-oxopropyl)phosphanium


Mass: 998.630 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H48N7O23P4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MCSG1 G4 (291317g4): 100mM Potassium tartrate, 20% PEG3350, 8mM NADP, protein conc. 20.8mg/mL, cryo 20% ethylene glycol: puck ID opk4-15

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2017
RadiationMonochromator: double crystal si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 44832 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.158 % / Biso Wilson estimate: 12.93 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.051 / Net I/σ(I): 30
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.45-1.497.150.5743.4432800.8630.619100
1.49-1.538.4490.4644.8131620.9380.494100
1.53-1.579.2270.3646.5130780.9680.385100
1.57-1.6210.3440.2978.530040.9760.312100
1.62-1.6710.8590.2510.3829070.9860.263100
1.67-1.7310.8190.20212.928360.990.213100
1.73-1.810.8840.15915.9627150.9940.167100
1.8-1.8710.8540.11621.4326320.9970.121100
1.87-1.9610.840.09126.6425390.9970.095100
1.96-2.0510.8590.06933.4324290.9990.072100
2.05-2.1610.8060.05539.8223140.9990.058100
2.16-2.2910.7950.04646.1521910.9990.049100
2.29-2.4510.8130.04150.6720830.9990.043100
2.45-2.6510.7280.03755.6619250.9990.039100
2.65-2.910.5910.03361.7717930.9990.035100
2.9-3.2410.4560.0367.7316360.9990.031100
3.24-3.7410.3740.02774.06145710.02899.9
3.74-4.5910.2780.02478.8912530.9990.02599.9
4.59-6.4810.1550.02377.5100210.024100
6.48-509.0890.02276.5959610.02399.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(DEV_2744: ???)refinement
XSCALEdata scaling
Cootmodel building
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5idx

5idx


Resolution: 1.45→34 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.72
RfactorNum. reflection% reflection
Rfree0.164 1998 4.46 %
Rwork0.148 --
obs0.149 44828 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 17.93 Å2
Refinement stepCycle: LAST / Resolution: 1.45→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1872 0 72 358 2302
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062015
X-RAY DIFFRACTIONf_angle_d1.1462756
X-RAY DIFFRACTIONf_dihedral_angle_d18.786726
X-RAY DIFFRACTIONf_chiral_restr0.081324
X-RAY DIFFRACTIONf_plane_restr0.006359
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4501-1.48630.17651330.18993029X-RAY DIFFRACTION100
1.4863-1.52650.22631390.17843013X-RAY DIFFRACTION100
1.5265-1.57140.19011300.16212997X-RAY DIFFRACTION100
1.5714-1.62220.18911230.15343007X-RAY DIFFRACTION100
1.6222-1.68010.18171550.15463004X-RAY DIFFRACTION100
1.6801-1.74740.14961330.15263022X-RAY DIFFRACTION100
1.7474-1.82690.17121460.14863041X-RAY DIFFRACTION100
1.8269-1.92320.14751410.14523016X-RAY DIFFRACTION100
1.9232-2.04370.15721350.14773055X-RAY DIFFRACTION100
2.0437-2.20150.16251390.14663066X-RAY DIFFRACTION100
2.2015-2.4230.15231590.14353042X-RAY DIFFRACTION100
2.423-2.77350.1661510.14823098X-RAY DIFFRACTION100
2.7735-3.49370.15611690.14213115X-RAY DIFFRACTION100
3.4937-33.7730.16321450.14143325X-RAY DIFFRACTION100
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)
14.2985-0.4465-1.84311.36931.11423.29330.0523-0.1694-0.15730.0298-0.04220.15910.1799-0.08630.01920.1209-0.0332-0.04410.08980.02070.1295-19.9732-18.858-11.7063
21.35310.1553-0.1531.04820.04310.7638-0.0010.1077-0.0561-0.18680.03310.01850.0937-0.1131-0.02650.1596-0.0101-0.04220.0951-0.00980.1007-14.1569-19.8614-21.3174
38.24950.6676-0.80111.1238-0.02921.43480.00960.4981-0.1145-0.18880.0946-0.0736-0.0397-0.0158-0.0890.15870.0103-0.00970.0743-0.01740.0911-5.3948-4.5285-22.855
41.03890.0363-0.1481.0061-0.11190.92060.0091-0.00890.035-0.05740.02360.0076-0.0016-0.0319-0.03570.08660.0039-0.01330.0589-0.00340.0628-6.8357-6.83-11.1998
57.6117-3.8955-1.43684.73520.49612.13880.14930.12160.257-0.2197-0.0943-0.1718-0.2288-0.0524-0.0640.2339-0.01220.05240.1289-0.00380.16489.9032-24.4805-15.6026
66.9127-5.1285-6.57027.10185.72337.0059-0.2181-0.5140.1235-0.09850.399-0.35330.02930.5603-0.16440.1623-0.0062-0.00650.14170.01230.167411.9045-26.964-6.2217
72.3475-0.91070.08220.9702-0.02810.33730.0028-0.0513-0.0375-0.01230.02440.00930.0248-0.0194-0.0240.10530.0015-0.00640.09070.0080.0705-8.0428-13.9979-2.5661
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 0 THROUGH 17 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 18 THROUGH 96 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 97 THROUGH 130 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 131 THROUGH 188 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 189 THROUGH 202 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 203 THROUGH 216 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 217 THROUGH 259 )

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