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- PDB-5ig2: Crystal structure of a short chain dehydrogenase/reductase SDR fr... -

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Basic information

Entry
Database: PDB / ID: 5ig2
TitleCrystal structure of a short chain dehydrogenase/reductase SDR from Burkholderia phymatum in complex with 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, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding
Similarity search - Function
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
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Short-chain dehydrogenase/reductase SDR
Similarity search - Component
Biological speciesBurkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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 in complex with NAD
Authors: Mayclin, S.J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 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
C: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9739
Polymers94,8063
Non-polymers2,1676
Water15,133840
1
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)193,94618
Polymers189,6116
Non-polymers4,33512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area25990 Å2
ΔGint-183 kcal/mol
Surface area58470 Å2
MethodPISA
2
A: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6496
Polymers63,2042
Non-polymers1,4454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area8050 Å2
ΔGint-61 kcal/mol
Surface area19660 Å2
MethodPISA
3
B: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6496
Polymers63,2042
Non-polymers1,4454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-60 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.520, 187.790, 108.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-454-

HOH

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Components

#1: Protein Short-chain dehydrogenase/reductase SDR


Mass: 31601.887 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia phymatum (strain DSM 17167 / STM815) (bacteria)
Strain: DSM 17167 / STM815 / Gene: Bphy_1038 / Plasmid: BuphA.00010.n.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B2JGP2
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / 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: 2.24 Å3/Da / Density % sol: 45 % / Mosaicity: 0.24 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: MCSG1 C4 (269066c4): 170mM Ammonium acetate, 85mM Sodium acetate:HCl pH4.6, 25.5% (w/v) PEG4000, 15% (v/v) Glycerol, 4mM NAD; direct cryo; puck kxt5-2

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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 / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→46.895 Å / Num. obs: 78892 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.22 % / Biso Wilson estimate: 18.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.071 / Χ2: 0.973 / Net I/σ(I): 20.63 / Num. measured all: 490706
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.856.230.5423.6935805575357500.8860.59199.9
1.85-1.90.4054.8135171564456430.9330.441100
1.9-1.950.3365.8534099547554740.9530.366100
1.95-2.010.2597.4433217532353190.9660.28399.9
2.01-2.080.2079.1332099514851470.9780.225100
2.08-2.150.16111.5131411502250200.9860.176100
2.15-2.230.13213.7530279484048400.990.144100
2.23-2.320.11415.5729229467546730.9930.125100
2.32-2.430.09218.527752443044300.9950.101100
2.43-2.550.08120.7826903429942990.9960.088100
2.55-2.680.06923.9425514407540750.9970.075100
2.68-2.850.05927.2424324388938880.9980.064100
2.85-3.040.05131.0722623362536250.9980.055100
3.04-3.290.04336.4921065338333830.9980.047100
3.29-3.60.03543.1919450314331420.9990.039100
3.6-4.020.03247.0717475284628430.9990.03599.9
4.02-4.650.02751.715537253525310.9990.02999.8
4.65-5.690.02551.7513198215921570.9990.02899.9
5.69-8.050.02550.9810153168916850.9990.02799.8
8.05-46.8950.02156.34540299796810.02397.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.2data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3tjr

3tjr


Resolution: 1.8→46.895 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.89 / Stereochemistry target values: LS_WUNIT_K1
RfactorNum. reflection% reflection
Rfree0.1772 1674 2.12 %
Rwork0.1411 77190 -
obs0.1419 78864 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.53 Å2 / Biso mean: 22.7617 Å2 / Biso min: 7.44 Å2
Refinement stepCycle: final / Resolution: 1.8→46.895 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6141 0 144 845 7130
Biso mean--18.46 33.54 -
Num. residues----838
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066499
X-RAY DIFFRACTIONf_angle_d0.7778887
X-RAY DIFFRACTIONf_chiral_restr0.0471038
X-RAY DIFFRACTIONf_plane_restr0.0051223
X-RAY DIFFRACTIONf_dihedral_angle_d14.4673890
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.8530.27151280.238263186446
1.853-1.91280.21411320.206264016533
1.9128-1.98120.19371460.189163826528
1.9812-2.06050.18661340.177963706504
2.0605-2.15420.2161500.168363646514
2.1542-2.26780.19691410.158364066547
2.2678-2.40990.17241240.149764206544
2.4099-2.5960.18821410.145264026543
2.596-2.85720.18581460.1464686614
2.8572-3.27050.19871500.129264466596
3.2705-4.12010.1641380.108365206658
4.1201-46.91120.12631440.111666936837
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)
11.41940.063-1.82730.5424-0.38852.9018-0.0363-0.09040.0624-0.01980.0765-0.0601-0.01470.0797-0.05610.0963-0.01080.00470.0781-0.00830.11622.369625.7991-3.905
20.69540.38620.31834.34530.78960.7829-0.01130.03010.0269-0.08940.00020.3971-0.0337-0.05910.03440.07140.008-0.0090.1210.00990.153511.679224.1416-3.1868
30.5413-0.03870.04171.6982-0.16030.4839-0.01360.040.0159-0.04160.0590.0419-0.0055-0.0071-0.05690.07560.0043-0.00080.1078-0.01610.106318.24719.0088-1.3835
40.85210.1201-0.47031.7325-0.3041.7459-0.0176-0.07010.04420.14590.0464-0.0994-0.08340.0241-0.01680.09090.0038-0.01760.116-0.02760.135824.40189.01574.5548
51.0547-0.10830.38633.2345-0.94765.07490.0624-0.15030.05750.14070.011-0.4773-0.47640.4560.02460.1157-0.0356-0.0050.167-0.0190.289133.303822.78241.1934
60.6059-1.10210.59213.8775-0.92960.56710.0264-0.05120.07910.1577-0.1274-0.5421-0.01060.21750.02280.0949-0.0049-0.02630.2116-0.01770.326839.51443.59023.7679
70.7544-0.0783-0.28210.28660.07920.11920.05430.0654-0.03460.0472-0.07710.121-0.1011-0.054-0.07690.1214-0.04930.07550.08410.02070.070416.251247.711619.8903
82.33020.38450.05922.1511-0.47312.12740.0805-0.0258-0.05860.1690.0050.1879-0.0236-0.0482-0.07860.0973-0.02110.04350.11090.00520.12511.399741.653211.653
92.3029-0.12990.33666.8306-4.20863.22630.10730.06190.04150.11730.13570.50810.0235-0.2994-0.18090.1446-0.00830.06090.1682-0.0090.16346.419148.259410.3079
102.7344-0.31320.45282.5125-3.08477.2140.1507-0.13080.18820.39820.19280.6125-0.2786-0.5206-0.2550.16690.00910.10570.1905-0.0230.28943.606155.191714.9807
110.99310.3452-0.23771.2111-0.36911.580.0825-0.05590.13720.128-0.01610.1372-0.0717-0.0808-0.05240.0999-0.00250.03270.08880.00460.112420.508158.96596.3669
121.57280.09360.012.25060.09891.65750.05910.0048-0.0444-0.02440.04810.00590.00290.0334-0.03610.0778-0.02680.02580.08110.03540.094421.892750.42445.7421
130.531-0.3024-0.81831.8754-0.97053.03250.06450.3155-0.0206-0.53040.00590.28520.2245-0.2066-0.13010.2309-0.0616-0.05170.15670.00650.16119.944649.2859-13.036
140.6786-0.404-0.49143.51862.20153.82850.0319-0.1178-0.07840.32030.0381-0.11060.26390.21730.04130.108-0.0264-0.00720.14910.02850.111827.075343.077412.4614
153.33171.0031-2.51832.0476-1.21982.51710.1496-0.07870.00910.0332-0.1016-0.1574-0.02460.17230.02420.0809-0.0038-0.03030.14630.00590.159838.684756.89223.6432
161.37060.2409-0.55480.0539-0.18491.6394-0.13750.09030.37120.0878-0.0060.0273-0.43770.0706-0.34120.174-0.02190.0410.13660.12040.197232.518983.9638-14.9793
171.49140.8951-0.00562.8868-0.79272.0735-0.02730.1170.31950.04180.08890.3542-0.4887-0.1779-0.05580.24190.04770.00960.17510.0850.269521.737687.1186-15.7329
180.71990.1888-0.00831.3122-0.6141.74460.04910.06680.1227-0.03850.01420.112-0.1116-0.0552-0.04470.09270.01550.02950.10130.02850.150424.984571.101-7.5575
191.96520.48150.42432.0682-0.25561.43930.0879-0.04650.48430.17140.0187-0.0198-0.3026-0.0832-0.1450.19290.02130.05050.10520.06390.210128.669478.4011-3.4036
201.55480.6095-1.07360.6197-0.71692.42920.1266-0.03890.41130.3338-0.00320.2506-0.5185-0.0966-0.09250.29380.05460.0950.15020.01530.344224.525481.9534.13
210.96750.54570.42092.8469-2.38834.55590.1293-0.08070.17190.2943-0.1855-0.0667-0.27590.17240.09330.1238-0.01070.00110.15080.00070.196639.254768.00286.8075
220.3893-1.03150.13853.30.0011.1994-0.009-0.0871-0.04210.11090.1011-0.1597-0.02580.0365-0.03980.1177-0.01820.02080.1397-0.00830.160120.569215.7246.4039
235.48881.2474-1.68831.952-0.73891.4756-0.11470.2788-0.0323-0.07880.04460.1091-0.0108-0.0171-0.04690.0992-0.01490.00760.11360.00850.101918.064448.38632.1137
241.67170.51851.56672.934-0.58682.81280.0471-0.01260.29030.13220.00330.0978-0.3195-0.1868-0.00110.15340.02790.06640.14540.01990.268523.979981.6386-2.6659
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 39 )A1 - 39
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 81 )A40 - 81
3X-RAY DIFFRACTION3chain 'A' and (resid 82 through 132 )A82 - 132
4X-RAY DIFFRACTION4chain 'A' and (resid 133 through 228 )A133 - 228
5X-RAY DIFFRACTION5chain 'A' and (resid 229 through 247 )A229 - 247
6X-RAY DIFFRACTION6chain 'A' and (resid 248 through 278 )A248 - 278
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 16 )B1 - 16
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 52 )B17 - 52
9X-RAY DIFFRACTION9chain 'B' and (resid 53 through 66 )B53 - 66
10X-RAY DIFFRACTION10chain 'B' and (resid 67 through 81 )B67 - 81
11X-RAY DIFFRACTION11chain 'B' and (resid 82 through 177 )B82 - 177
12X-RAY DIFFRACTION12chain 'B' and (resid 178 through 201 )B178 - 201
13X-RAY DIFFRACTION13chain 'B' and (resid 202 through 228 )B202 - 228
14X-RAY DIFFRACTION14chain 'B' and (resid 229 through 246 )B229 - 246
15X-RAY DIFFRACTION15chain 'B' and (resid 247 through 281 )B247 - 281
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 29 )C1 - 29
17X-RAY DIFFRACTION17chain 'C' and (resid 30 through 66 )C30 - 66
18X-RAY DIFFRACTION18chain 'C' and (resid 67 through 177 )C67 - 177
19X-RAY DIFFRACTION19chain 'C' and (resid 178 through 201 )C178 - 201
20X-RAY DIFFRACTION20chain 'C' and (resid 202 through 246 )C202 - 246
21X-RAY DIFFRACTION21chain 'C' and (resid 247 through 279 )C247 - 279
22X-RAY DIFFRACTION22chain 'A' and resid ' 301 'A301
23X-RAY DIFFRACTION23chain 'B' and resid ' 301 'B301
24X-RAY DIFFRACTION24chain 'C' and resid ' 301 'C301

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