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- PDB-5idx: Crystal structure of an oxidoreductase from Burkholderia vietnamiensis -

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Basic information

Entry
Database: PDB / ID: 5idx
TitleCrystal structure of an oxidoreductase from Burkholderia vietnamiensis
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / SSGCID / short chain dehydrogenase/reductase family / Burkholderia vietnamiensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyEnoyl-(Acyl carrier protein) reductase / 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: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of an oxidoreductase from Burkholderia vietnamiensis
Authors: Mayclin, S.J. / Abendroth, J. / 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

Downloads & links

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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)56,0999
Polymers55,4272
Non-polymers6727
Water8,053447
1
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)112,19918
Polymers110,8544
Non-polymers1,34514
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area18240 Å2
ΔGint-341 kcal/mol
Surface area35660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.750, 110.750, 110.050
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 27713.504 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_2377 / Plasmid: BuviA.00010.k.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4JGH3
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 447 / 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: 3.05 Å3/Da / Density % sol: 60 % / Mosaicity: 0.33 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: MCSG1 C8 (269601c8): 200mM Ammonium sulfate, 100mM Sodium citrate-HCl pH5.6, 25% PEG4000, 4mM NAD; protein conc. 21.43mg/mL; 20% eg cryo; puck dom8-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 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: 0.97872 Å / Relative weight: 1
ReflectionHighest resolution: 1.95 Å / Num. obs: 50463 / % possible obs: 100 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.078 / Χ2: 1.055 / Net I/σ(I): 23.21 / Num. measured all: 522083
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.95-20.5694.639301367836780.9310.597100
2-2.060.3936.6138210357335730.9620.413100
2.06-2.120.3347.8837092348334830.9760.35100
2.12-2.180.2759.3935974339133910.9810.289100
2.18-2.250.24110.7834834328832870.9850.253100
2.25-2.330.18513.7333431318331830.990.194100
2.33-2.420.16115.5832175307430740.9930.169100
2.42-2.520.13518.1730911297429740.9950.141100
2.52-2.630.11720.4329386283728360.9960.123100
2.63-2.760.10123.328148273427330.9960.107100
2.76-2.910.08128.1326580261326130.9980.085100
2.91-3.080.06832.3924885246124590.9980.07199.9
3.08-3.30.05836.7923464232923290.9990.06100
3.3-3.560.04842.8621815218621850.9990.051100
3.56-3.90.04445.9720174201120110.9990.046100
3.9-4.360.03950.5518486183818380.9990.041100
4.36-5.030.03452.8316639164416440.9990.035100
5.03-6.170.03350.3314152139713970.9990.034100
6.17-8.720.02853.18108751117111710.029100
8.720.02552.48555167665810.02697.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXdev_2313refinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O5I

1o5i


Resolution: 1.95→45.165 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 1955 3.88 %
Rwork0.1605 48434 -
obs0.1619 50389 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.3 Å2 / Biso mean: 31.5912 Å2 / Biso min: 12.8 Å2
Refinement stepCycle: final / Resolution: 1.95→45.165 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 35 447 4209
Biso mean--70.9 38.61 -
Num. residues----524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063846
X-RAY DIFFRACTIONf_angle_d0.7135253
X-RAY DIFFRACTIONf_chiral_restr0.05623
X-RAY DIFFRACTIONf_plane_restr0.005696
X-RAY DIFFRACTIONf_dihedral_angle_d12.9452285
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.95-1.99870.26011480.210533873535
1.9987-2.05280.25981350.189434143549
2.0528-2.11320.251400.18334023542
2.1132-2.18140.21561610.179133743535
2.1814-2.25930.20371180.169134563574
2.2593-2.34980.17341490.158333903539
2.3498-2.45670.21171560.165834193575
2.4567-2.58620.21891550.166934093564
2.5862-2.74820.22871330.172434523585
2.7482-2.96040.19821640.170334263590
2.9604-3.25820.19041140.161835173631
3.2582-3.72950.18421390.151634933632
3.7295-4.6980.17271010.134335693670
4.698-45.17760.1731420.155537263868
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)
13.52120.9157-0.97614.3505-1.07372.1007-0.0641-0.2918-0.02430.1552-0.0783-0.2720.06970.26180.13770.1641-0.00540.02340.23360.03440.186418.649211.785423.6457
21.4136-0.7782-0.68073.48891.62351.9069-0.0348-0.05060.09930.0319-0.0559-0.04170.05950.01950.08390.1407-0.02920.01540.20250.03380.15512.292220.155722.2109
32.4946-0.3243-0.20721.4328-0.66292.8272-0.045-0.47650.32110.28120.0258-0.1269-0.35910.16920.03670.2855-0.05160.02830.2836-0.01320.26192.105811.254937.3825
42.81630.25790.17872.9032-0.85662.1818-0.0110.16260.3956-0.1854-0.0114-0.0243-0.27940.07950.01290.2282-0.01150.01680.15470.0350.2136-19.078946.705117.6997
52.5613-1.2403-1.65222.14951.13042.66060.04250.15560.0914-0.1082-0.0716-0.0804-0.00230.05710.03330.1217-0.0165-0.00420.16110.03620.1287-9.011431.53522.0933
61.6130.5475-0.97592.70181.04943.76370.01180.7139-0.1265-0.96930.1147-0.5054-0.0470.3094-0.01120.43650.0120.09480.4302-0.00470.2747-19.872728.30552.1822
71.79410.0370.33412.0447-0.04561.286-0.03860.2433-0.0815-0.30620.0113-0.0320.09740.0463-0.00120.1753-0.01380.03640.1740.0240.1421-24.809624.935317.4996
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 86 )A10 - 86
2X-RAY DIFFRACTION2chain 'A' and (resid 87 through 182 )A87 - 182
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 259 )A183 - 267
4X-RAY DIFFRACTION4chain 'B' and (resid 9 through 86 )B9 - 86
5X-RAY DIFFRACTION5chain 'B' and (resid 87 through 182 )B87 - 182
6X-RAY DIFFRACTION6chain 'B' and (resid 183 through 204 )B183 - 204
7X-RAY DIFFRACTION7chain 'B' and (resid 205 through 259 )B205 - 267

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