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- PDB-6d9y: Crystal structure of a short chain dehydrogenase/reductase SDR fr... -

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Basic information

Entry
Database: PDB / ID: 6d9y
TitleCrystal structure of a short chain dehydrogenase/reductase SDR from Burkholderia phymatum with partially occupied NAD
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / SSGCID / short chain dehydrogenase/reductase family / NAD / Burkholderia phymatum / 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 / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
FORMIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / OXAMIC ACID / Short-chain dehydrogenase/reductase SDR
Similarity search - Component
Biological speciesParaburkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.3 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 phymatum with partially occupied NAD
Authors: Mayclin, S.J. / Abendroth, J. / Horanyi, P.S. / Lorimer, D.D. / Edwards, T.E.
History
DepositionApr 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 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
B: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,53013
Polymers55,2452
Non-polymers1,28511
Water11,385632
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)113,06026
Polymers110,4914
Non-polymers2,57022
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area20670 Å2
ΔGint-88 kcal/mol
Surface area31360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.900, 131.900, 66.510
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 27622.654 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paraburkholderia phymatum (strain DSM 17167 / CIP 108236 / LMG 21445 / STM815) (bacteria)
Strain: DSM 17167 / CIP 108236 / LMG 21445 / STM815 / Gene: Bphy_3470 / Plasmid: BuphA.00010.x.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B2JLJ0, Oxidoreductases; Acting on the CH-CH group of donors; With a flavin as acceptor

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Non-polymers , 5 types, 643 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-OXM / OXAMIC ACID


Mass: 89.050 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3NO3
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 632 / 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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 21.18 mg/mL BuphA.00010.x.B1.PS37816 + 4 mM NADP + MORPHEUS G2 (269916g2) (10% w/v PEG8000, 20% v/v ethylene glycol, 100 mM MES imidazole, pH 6.5, 20 mM sodium formate, 20 mM ammonium ...Details: 21.18 mg/mL BuphA.00010.x.B1.PS37816 + 4 mM NADP + MORPHEUS G2 (269916g2) (10% w/v PEG8000, 20% v/v ethylene glycol, 100 mM MES imidazole, pH 6.5, 20 mM sodium formate, 20 mM ammonium acetate, 20 mM trisodium citrate, 20 mM sodium potassium-L-tartrate, 20 mM sodium oxamate), direct cryoprotection, puck xut9-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 16, 2016
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 143395 / % possible obs: 100 % / Redundancy: 9.635 % / Biso Wilson estimate: 9.25 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rrim(I) all: 0.108 / Χ2: 0.958 / Net I/σ(I): 13.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.3-1.338.3950.5653.69105200.8810.602100
1.33-1.379.5410.514.42101840.9130.539100
1.37-1.419.6610.4325.299460.9320.457100
1.41-1.459.6870.3696.0696990.9520.39100
1.45-1.59.7270.2927.4693640.970.309100
1.5-1.559.750.2399.0290990.9780.253100
1.55-1.619.7670.20310.3487720.9840.214100
1.61-1.689.8040.17611.7684600.9880.186100
1.68-1.759.8110.1513.5781070.990.159100
1.75-1.849.8260.1315.3177730.9920.137100
1.84-1.949.8490.11117.7173960.9940.117100
1.94-2.069.8440.0972070170.9950.103100
2.06-2.29.8380.08821.8766170.9950.093100
2.2-2.379.8250.08423.2961680.9950.088100
2.37-2.69.8220.07924.6457020.9950.084100
2.6-2.919.790.07625.7551820.9960.08100
2.91-3.369.7470.07426.9546000.9960.078100
3.36-4.119.6570.07328.0839220.9960.07799.9
4.11-5.819.4830.07127.9630820.9960.07599.5
5.81-508.6830.07526.5517850.9950.0897.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4NBV

4nbv


Resolution: 1.3→50 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 13.89
RfactorNum. reflection% reflection
Rfree0.152 1996 1.39 %
Rwork0.1433 --
obs0.1434 143315 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.03 Å2 / Biso mean: 16.2702 Å2 / Biso min: 4.51 Å2
Refinement stepCycle: final / Resolution: 1.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3704 0 85 661 4450
Biso mean--47.96 29.86 -
Num. residues----502
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.2999-1.33240.21021340.18611000610140
1.3324-1.36850.18661430.1722994810091
1.3685-1.40870.17461360.1634999010126
1.4087-1.45420.16821580.1551999610154
1.4542-1.50620.12451280.14471000210130
1.5062-1.56650.16021370.13851001410151
1.5665-1.63780.15331330.13451003610169
1.6378-1.72410.15231450.13231004510190
1.7241-1.83210.14061460.13661008110227
1.8321-1.97360.15981530.13721007010223
1.9736-2.17210.13571260.13551013810264
2.1721-2.48630.1511450.13671017010315
2.4863-3.1320.14521470.14511025710404
3.132-31.0980.14951650.14391056610731
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)
12.8182-1.1495-1.09613.2760.17231.81740.0280.1758-0.1863-0.1284-0.10520.20330.1183-0.06120.00430.0422-0.0178-0.00970.0883-0.01410.0651137.040621.32662.2111
21.3184-0.05220.3671.3040.35751.68170.00710.12090.0426-0.1432-0.10090.3089-0.1345-0.29460.07870.06730.0183-0.00440.1493-0.00870.1255129.541727.5279-0.5327
32.96311.9150.23355.63491.98411.60510.06410.05330.13120.1777-0.12180.37520.0983-0.15540.04780.07830.01930.01240.13080.03590.0897130.355933.62266.4186
40.6160.3059-0.28110.4023-0.11760.4226-0.0010.03760.06470.01160.02540.0665-0.0257-0.079-0.0330.05390.00430.00740.06720.00510.0669144.057837.66046.1077
51.78620.1880.44050.87890.29980.9172-0.11010.29990.1431-0.17670.02570.0847-0.1553-0.15830.17420.09340.0079-0.01040.12150.01630.0883145.863330.7653-2.1568
61.3681-0.1355-0.29951.75470.84560.9454-0.07770.59180.9568-0.33450.18070.1408-0.451-0.2245-0.05280.20090.003-0.03170.22510.14230.2979149.879332.7348-18.1644
70.65410.02910.03270.3321-0.09550.99-0.01790.0031-0.01240.01270.0202-0.0132-0.015-0.07470.02920.05140.00420.00530.0508-0.00190.0758150.458423.6816-0.2354
81.5966-0.8776-0.44462.8697-0.12891.91030.0117-0.08050.23090.06650.0499-0.28190.0380.2546-0.04980.099-0.0283-0.01610.0782-0.01550.1032175.856658.42745.3571
92.2541-0.2785-0.34370.79250.08291.35520.0203-0.10940.08590.10740.0369-0.0127-0.08140.034-0.06470.121-0.0198-0.00120.0538-0.02060.0984171.929260.64659.9285
103.31750.4320.43721.10780.2871.03030.035-0.16980.24910.10780.0065-0.0367-0.15790.0787-0.05210.208-0.00260.01750.0857-0.02570.1334166.41965.371713.79
117.04474.3225-2.86374.5766-1.90061.8906-0.10420.06030.3991-0.08820.14130.2722-0.1233-0.1-0.04970.170.01860.00740.04910.00460.1327159.484168.11622.9774
120.43530.2927-0.31510.8101-0.52910.81690.0434-0.02610.05630.0778-0.02430.0406-0.093-0.0074-0.02720.0724-0.00220.00220.0491-0.00170.0664158.09449.3456.1882
131.55820.08120.14871.36120.24980.047-0.0337-0.29540.02410.41770.0078-0.0194-0.2507-0.18390.05960.17040.0120.00340.0992-0.00630.0801165.839948.62056.9361
141.0133-0.0010.76391.29290.16890.77740.0255-0.175-0.02380.23370.00880.0492-0.0384-0.1343-0.00720.0833-0.00250.0130.0882-0.00620.0777172.086542.13799.1213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 18 )A0 - 18
2X-RAY DIFFRACTION2chain 'A' and (resid 19 through 54 )A19 - 54
3X-RAY DIFFRACTION3chain 'A' and (resid 55 through 67 )A55 - 67
4X-RAY DIFFRACTION4chain 'A' and (resid 68 through 174 )A68 - 174
5X-RAY DIFFRACTION5chain 'A' and (resid 175 through 199 )A175 - 199
6X-RAY DIFFRACTION6chain 'A' and (resid 200 through 217 )A200 - 217
7X-RAY DIFFRACTION7chain 'A' and (resid 218 through 250 )A218 - 250
8X-RAY DIFFRACTION8chain 'B' and (resid 0 through 18 )B0 - 18
9X-RAY DIFFRACTION9chain 'B' and (resid 19 through 41 )B19 - 41
10X-RAY DIFFRACTION10chain 'B' and (resid 42 through 67 )B42 - 67
11X-RAY DIFFRACTION11chain 'B' and (resid 68 through 82 )B68 - 82
12X-RAY DIFFRACTION12chain 'B' and (resid 83 through 174 )B83 - 174
13X-RAY DIFFRACTION13chain 'B' and (resid 175 through 199 )B175 - 199
14X-RAY DIFFRACTION14chain 'B' and (resid 200 through 250 )B200 - 250

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