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- PDB-5k9z: Crystal Structure of putative short-chain dehydrogenase/reductase... -

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Basic information

Entry
Database: PDB / ID: 5k9z
TitleCrystal Structure of putative short-chain dehydrogenase/reductase from Burkholderia xenovorans LB400
ComponentsPutative short-chain dehydrogenase/reductaseShort-chain dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase/reductase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homologyEnoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / oxidoreductase activity / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Putative short-chain dehydrogenase/reductase
Function and homology information
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal Structure of putative short-chain dehydrogenase/reductase from Burkholderia xenovorans LB400
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Delker, S.L. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionJun 1, 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

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Assembly

Deposited unit
A: Putative short-chain dehydrogenase/reductase
B: Putative short-chain dehydrogenase/reductase
C: Putative short-chain dehydrogenase/reductase
D: Putative short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,1059
Polymers116,6444
Non-polymers4605
Water9,458525
1
A: Putative short-chain dehydrogenase/reductase
C: Putative short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5995
Polymers58,3222
Non-polymers2763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-26 kcal/mol
Surface area22160 Å2
MethodPISA
2
B: Putative short-chain dehydrogenase/reductase
D: Putative short-chain dehydrogenase/reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5064
Polymers58,3222
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3380 Å2
ΔGint-26 kcal/mol
Surface area22140 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19340 Å2
ΔGint-122 kcal/mol
Surface area31870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.290, 54.760, 115.730
Angle α, β, γ (deg.)90.000, 100.250, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 11:48 or (resid 49 and (name...
21(chain B and ((resid 11 and (name N or name...
31(chain C and ((resid 11 and (name N or name...
41(chain D and (resid 11:49 or resid 51:56 or resid...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 11:48 or (resid 49 and (name...A11 - 48
121(chain A and (resid 11:48 or (resid 49 and (name...A49
131(chain A and (resid 11:48 or (resid 49 and (name...A11 - 300
141(chain A and (resid 11:48 or (resid 49 and (name...A11 - 300
151(chain A and (resid 11:48 or (resid 49 and (name...A11 - 300
161(chain A and (resid 11:48 or (resid 49 and (name...A11 - 300
211(chain B and ((resid 11 and (name N or name...B11
221(chain B and ((resid 11 and (name N or name...B10 - 300
231(chain B and ((resid 11 and (name N or name...B10 - 300
241(chain B and ((resid 11 and (name N or name...B10 - 300
251(chain B and ((resid 11 and (name N or name...B10 - 300
311(chain C and ((resid 11 and (name N or name...C11
321(chain C and ((resid 11 and (name N or name...C10 - 300
331(chain C and ((resid 11 and (name N or name...C10 - 300
341(chain C and ((resid 11 and (name N or name...C10 - 300
351(chain C and ((resid 11 and (name N or name...C10 - 300
411(chain D and (resid 11:49 or resid 51:56 or resid...D11 - 49
421(chain D and (resid 11:49 or resid 51:56 or resid...D51 - 56
431(chain D and (resid 11:49 or resid 51:56 or resid...D58 - 87
441(chain D and (resid 11:49 or resid 51:56 or resid...D89 - 106
451(chain D and (resid 11:49 or resid 51:56 or resid...D108 - 162
461(chain D and (resid 11:49 or resid 51:56 or resid...D164 - 168
471(chain D and (resid 11:49 or resid 51:56 or resid...D170 - 188
481(chain D and (resid 11:49 or resid 51:56 or resid...D190 - 193
491(chain D and (resid 11:49 or resid 51:56 or resid...D217 - 225
4101(chain D and (resid 11:49 or resid 51:56 or resid...D227 - 258
4111(chain D and (resid 11:49 or resid 51:56 or resid...D261
4121(chain D and (resid 11:49 or resid 51:56 or resid...D265 - 267
4131(chain D and (resid 11:49 or resid 51:56 or resid...D269 - 272
4141(chain D and (resid 11:49 or resid 51:56 or resid...D274 - 275

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Components

#1: Protein
Putative short-chain dehydrogenase/reductase / Short-chain dehydrogenase / BuxeA.00010.p.B1


Mass: 29161.117 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: Bxe_C0620 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13HC1
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 525 / 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: 2.31 Å3/Da / Density % sol: 46.68 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus h11 (270147h11): 10% Peg 4000, 20% glycerol, 0.02M amino acid (0.2 M sodium l-glutamate, 0.2 M dl-alanine, 0.2 M glycine, 0.2 M dl-lysine HCl, 0.2 M dl-serine), 0.1M bicine/trizma ...Details: Morpheus h11 (270147h11): 10% Peg 4000, 20% glycerol, 0.02M amino acid (0.2 M sodium l-glutamate, 0.2 M dl-alanine, 0.2 M glycine, 0.2 M dl-lysine HCl, 0.2 M dl-serine), 0.1M bicine/trizma ph 8.5; cryo: direct; BuxeA.00010.p.B1.ps37825 at 18.15 mg/ml, puck sbt3-10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 13, 2016 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 71539 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 20.64 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.62
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.050.5083.14198.2
2.05-2.110.4153.8198.3
2.11-2.170.3344.53198.3
2.17-2.240.2775.47198.5
2.24-2.310.2436.04198.5
2.31-2.390.2057198.8
2.39-2.480.197.62198.6
2.48-2.580.1598.76199.1
2.58-2.70.1419.76198.6
2.7-2.830.11211.77199.3
2.83-2.980.08814.17199.1
2.98-3.160.07516.61199.4
3.16-3.380.06119.79199.5
3.38-3.650.05123.63199.2
3.65-40.04326.93199.5
4-4.470.0428.78199.2
4.47-5.160.03730.42199
5.16-6.320.03927.23199.8
6.32-8.940.03232.43199.1
8.94-500.0334.67197.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2386refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1nff

1nff


Resolution: 2→44.173 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.13
RfactorNum. reflection% reflection
Rfree0.2002 1981 2.77 %
Rwork0.166 --
obs0.1669 71532 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 108.36 Å2 / Biso mean: 28.7699 Å2 / Biso min: 5.41 Å2
Refinement stepCycle: final / Resolution: 2→44.173 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7160 0 30 538 7728
Biso mean--50.34 33.12 -
Num. residues----1022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077409
X-RAY DIFFRACTIONf_angle_d0.77810106
X-RAY DIFFRACTIONf_chiral_restr0.051214
X-RAY DIFFRACTIONf_plane_restr0.0061327
X-RAY DIFFRACTIONf_dihedral_angle_d12.6224385
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3750X-RAY DIFFRACTION8.145TORSIONAL
12B3750X-RAY DIFFRACTION8.145TORSIONAL
13C3750X-RAY DIFFRACTION8.145TORSIONAL
14D3750X-RAY DIFFRACTION8.145TORSIONAL
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 (%)
2-2.050.29441240.22014907503198
2.05-2.10550.25131390.20684907504698
2.1055-2.16740.22811590.19234878503798
2.1674-2.23740.2111380.18084899503798
2.2374-2.31730.24481570.17844925508298
2.3173-2.41010.221490.17124937508699
2.4101-2.51980.19791190.17074941506099
2.5198-2.65260.22991360.1784934507099
2.6526-2.81880.20351350.17494963509899
2.8188-3.03640.19171600.16825007516799
3.0364-3.34180.22631370.16474998513599
3.3418-3.82520.18361540.14665000515499
3.8252-4.81840.15851420.13675061520399
4.8184-44.1840.1641320.16185194532699
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)
14.748-0.76830.90392.4041-0.7252.24280.03440.1092-0.2214-0.03970.00140.39140.202-0.6911-0.02530.1278-0.0638-0.03370.4050.00270.3001-39.0742-10.95477.4195
21.2244-0.27530.11671.2454-0.18851.3375-0.00060.1061-0.0773-0.09430.04090.23940.0721-0.2416-0.04040.1339-0.0298-0.00820.16080.00740.1393-23.044-7.6137.3511
35.02551.0677-1.57193.59020.49375.2262-0.0789-0.3633-0.60140.4855-0.05090.02210.4548-0.45780.04460.1899-0.04190.01920.23370.04180.1803-31.5302-7.477521.0713
42.70682.1928-1.5872.54640.55865.3994-0.05540.07030.1453-0.0499-0.02260.08960.1418-0.19040.09250.09930.00270.04880.17890.01610.1431-27.9355-0.318323.1235
53.92470.1722-0.13784.5129-2.60257.50150.07820.0465-0.1163-0.17270.0614-0.2650.6546-0.2196-0.12650.31870.05710.10860.17390.06960.1994-18.7015-7.674350.7214
63.4619-0.1410.49115.2199-1.11255.711-0.0387-0.13830.2318-0.0540.1216-0.4768-0.18020.6632-0.02140.1485-0.01780.0380.2155-0.0890.194415.3846-5.017415.185
71.0761-0.42340.19711.1467-0.25560.9487-0.06730.0353-0.01860.05360.0756-0.04870.05750.0897-0.00950.1788-0.00310.0210.1122-0.01660.1051-0.3564-9.500112.5178
82.46230.54530.11020.12250.03760.0744-0.05180.44110.4617-0.80510.18990.04570.16340.0398-0.06730.4308-0.02720.06360.21550.01630.21050.9333.886812.9946
91.6662-0.4005-0.39951.48510.67781.24730.00660.10220.2864-0.07460.1728-0.1301-0.41380.0657-0.1670.3549-0.02190.05340.146-0.0120.1617-1.41219.75425.0709
104.30431.6787-1.42546.4679-0.8537.2082-0.10310.1334-0.28810.01410.122-0.54810.12940.6854-0.00350.23610.0492-0.00010.2274-0.07110.13899.61635.223343.8511
116.51251.8131-1.81434.8993-1.61118.28680.0713-0.61-0.25790.647-0.0946-0.30540.03290.74340.01320.32960.0436-0.0170.2161-0.03820.19139.22345.775254.3659
120.82170.25670.0460.75670.14560.7525-0.0156-0.04330.0080.04610.0663-0.0379-0.11030.0445-0.05010.2770.01740.05640.123-0.00430.1166-6.26159.919345.084
131.1308-0.23480.4270.1084-0.44052.29420.0175-0.322-0.37780.4670.1290.16750.348-0.0095-0.15090.50010.09590.080.28330.06050.2694-3.8924-7.442345.3854
141.8221-0.00720.74611.82880.69512.0196-0.0662-0.0629-0.13730.12390.1736-0.09630.17070.0626-0.09090.24970.02780.04910.114-0.01960.11280.913-2.17934.123
151.12390.6607-0.6384.48143.10135.54180.2721-0.1052-0.32430.53290.06580.05521.025-0.226-0.27430.5518-0.00580.06140.19120.04350.343-13.1942-23.365220.9183
163.47211.8811-0.58634.9498-0.57825.62440.09810.22550.0182-0.24570.04220.4992-0.112-1.1464-0.11940.17590.09590.03860.47910.01750.3139-43.09157.479433.1413
171.10640.3155-0.0921.45460.10981.3650.0044-0.00560.12390.11080.02110.3537-0.1534-0.4051-0.01050.24160.07280.0750.24680.02210.2039-31.7948.968641.549
183.8552-0.15891.50284.5975-0.01914.6035-0.15030.41080.4943-0.5582-0.0855-0.0956-0.3937-0.18110.17440.22410.07720.04840.2620.04270.1915-32.53547.889626.1577
194.1412-1.1449-0.68574.905-0.91035.9412-0.1253-0.0478-0.15910.06090.02940.0048-0.0562-0.26150.10020.12270.0281-0.0030.1685-0.00290.0713-28.37690.724825.4827
208.96660.514-0.46647.23791.64568.1334-0.05740.17610.15770.5939-0.0611-0.19160.0666-0.1830.120.2535-0.0672-0.01160.10480.08050.1233-9.67217.24762.4942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 58 )A11 - 58
2X-RAY DIFFRACTION2chain 'A' and (resid 59 through 182 )A59 - 182
3X-RAY DIFFRACTION3chain 'A' and (resid 183 through 236 )A183 - 236
4X-RAY DIFFRACTION4chain 'A' and (resid 237 through 258 )A237 - 258
5X-RAY DIFFRACTION5chain 'A' and (resid 259 through 276 )A259 - 276
6X-RAY DIFFRACTION6chain 'B' and (resid 10 through 58 )B10 - 58
7X-RAY DIFFRACTION7chain 'B' and (resid 59 through 182 )B59 - 182
8X-RAY DIFFRACTION8chain 'B' and (resid 183 through 204 )B183 - 204
9X-RAY DIFFRACTION9chain 'B' and (resid 205 through 275 )B205 - 275
10X-RAY DIFFRACTION10chain 'C' and (resid 10 through 37 )C10 - 37
11X-RAY DIFFRACTION11chain 'C' and (resid 38 through 58 )C38 - 58
12X-RAY DIFFRACTION12chain 'C' and (resid 59 through 182 )C59 - 182
13X-RAY DIFFRACTION13chain 'C' and (resid 183 through 216 )C183 - 216
14X-RAY DIFFRACTION14chain 'C' and (resid 217 through 257 )C217 - 257
15X-RAY DIFFRACTION15chain 'C' and (resid 258 through 275 )C258 - 275
16X-RAY DIFFRACTION16chain 'D' and (resid 10 through 37 )D10 - 37
17X-RAY DIFFRACTION17chain 'D' and (resid 38 through 182 )D38 - 182
18X-RAY DIFFRACTION18chain 'D' and (resid 183 through 236 )D183 - 236
19X-RAY DIFFRACTION19chain 'D' and (resid 237 through 258 )D237 - 258
20X-RAY DIFFRACTION20chain 'D' and (resid 259 through 277 )D259 - 277

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