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- PDB-5unl: Crystal structure of a D-beta-hydroxybutyrate dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 5unl
TitleCrystal structure of a D-beta-hydroxybutyrate dehydrogenase from Burkholderia multivorans
Components3-ketoacyl-ACP reductase
KeywordsOXIDOREDUCTASE / SSGCID / Burkholderia multivorans / short-chain alcohol / dehydrogenase / reductase / SDR / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NITRATE ION / :
Function and homology information
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a D-beta-hydroxybutyrate dehydrogenase from Burkholderia multivorans
Authors: Mayclin, S.J. / Dranow, D.M. / Lorimer, D. / Edwards, T.E.
History
DepositionJan 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 15, 2017Provider: 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: 3-ketoacyl-ACP reductase
B: 3-ketoacyl-ACP reductase
C: 3-ketoacyl-ACP reductase
D: 3-ketoacyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,34615
Polymers114,6634
Non-polymers68311
Water18,7901043
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14740 Å2
ΔGint-71 kcal/mol
Surface area33840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.380, 132.090, 64.530
Angle α, β, γ (deg.)90.000, 108.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
3-ketoacyl-ACP reductase


Mass: 28665.826 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (bacteria) / Gene: WM33_05200 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A1B4TPS8
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1043 / 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: 2.27 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: JCSG+ A12 (272912a12): 20% w/v PEG3350, 200mM Potassium nitrate: protein conc 18mg/mL: 20% eg: icw9-5

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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-300 / Detector: CCD / Date: Jun 22, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 121380 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.17 % / Biso Wilson estimate: 16.18 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Rrim(I) all: 0.074 / Χ2: 0.977 / Net I/σ(I): 13.99
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.65-1.694.2020.4972.8389160.8270.5798.8
1.69-1.744.210.3843.6487450.8890.4498.9
1.74-1.794.2310.3184.3584690.9180.36498.9
1.79-1.844.2250.2555.4281990.9450.29299
1.84-1.914.2350.196780090.9680.22599.1
1.91-1.974.2310.1588.4677540.9780.18299.3
1.97-2.054.2320.12610.4574170.9850.14599.2
2.05-2.134.2180.10112.5572400.9890.11799.2
2.13-2.224.2030.08414.7169100.9920.09799.3
2.22-2.334.2040.07516.3465750.9930.08699.4
2.33-2.464.1910.06618.2262700.9940.07699.3
2.46-2.614.1530.0619.8159590.9950.06999.3
2.61-2.794.1390.05521.6956190.9960.06499.3
2.79-3.014.10.04924.0851660.9960.05799
3.01-3.34.0410.04526.3747700.9970.05298.9
3.3-3.694.0280.04228.6643290.9970.04998.8
3.69-4.263.9830.043038550.9970.04699.4
4.26-5.2240.03830.232510.9980.04399.6
5.22-7.384.0220.03629.5425340.9980.04199.3
7.38-44.8623.8370.03430.8513930.9980.03998

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
Cootmodel building
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4nbv
Resolution: 1.65→50 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.09
RfactorNum. reflection% reflection
Rfree0.2077 1973 1.63 %
Rwork0.1752 --
obs0.1757 121308 99.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 70.9 Å2 / Biso mean: 23.0859 Å2 / Biso min: 8.15 Å2
Refinement stepCycle: final / Resolution: 1.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7668 0 48 1057 8773
Biso mean--35.24 33.24 -
Num. residues----1054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068004
X-RAY DIFFRACTIONf_angle_d0.81110890
X-RAY DIFFRACTIONf_chiral_restr0.0551274
X-RAY DIFFRACTIONf_plane_restr0.0051449
X-RAY DIFFRACTIONf_dihedral_angle_d17.3584846
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 99 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.65-1.69120.28961160.22758455
1.6912-1.73690.24471700.21478482
1.7369-1.78810.22261470.19868504
1.7881-1.84580.21711520.19268449
1.8458-1.91170.22841450.19078491
1.9117-1.98830.24311400.18888500
1.9883-2.07880.20871430.17728559
2.0788-2.18840.19731220.17398492
2.1884-2.32550.20731680.16918537
2.3255-2.5050.20631340.16888547
2.505-2.75710.22111220.17478562
2.7571-3.15590.20781050.16868551
3.1559-3.97580.2071690.1638549
3.9758-500.17151400.16828657
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.23520.50260.21863.74241.3082.1017-0.00240.078-0.0272-0.1131-0.0126-0.39590.06870.11870.01310.1819-0.01940.05920.10960.04010.178349.016115.3401-2.3666
24.99380.1102-1.21752.8330.24973.66340.1715-0.15110.05660.02-0.0648-0.5159-0.06190.3719-0.08610.186-0.0351-0.00440.110.03390.233250.939224.23791.6997
32.1971.15790.3045.73990.86764.8791-0.06150.09680.236-0.19550.0720.0158-0.1968-0.0170.0170.1225-0.0135-0.00070.12180.03070.143940.031725.0621-4.5666
41.8505-0.6374-1.79350.834-0.44573.94820.0891-0.2080.09470.0399-0.04750.019-0.36110.0311-0.06710.1735-0.0332-0.01310.1143-0.04550.158533.756722.045819.5927
52.9437-0.3056-2.36643.85882.73577.22180.02830.19280.2212-0.2017-0.170.2388-0.4375-0.30060.11130.13190.0149-0.00190.08990.03370.147431.944721.1906-3.3902
61.0524-0.03080.85390.476-0.57331.62930.01570.010.019-0.06470.01930.0013-0.05790.1-0.01930.12540.00290.01820.09-0.00950.115932.536710.92567.5641
72.0707-0.0392.7282.5357-0.80046.30650.2651-0.0032-0.2434-0.15550.0817-0.06390.08270.2014-0.33410.07530.00550.03310.08370.00190.111640.31988.22376.0648
86.4619-0.1292-5.59325.43430.90789.37970.1028-0.24230.291-0.1984-0.0557-0.5495-0.4177-0.1256-0.08360.1646-0.0161-0.05050.2274-0.05090.250245.956316.156224.154
92.6751.8462.25944.29225.26136.46920.1069-0.41930.00620.6992-0.0139-0.38360.40110.0388-0.11920.1872-0.0307-0.06650.32920.02980.212546.80976.196329.1365
101.23010.6442-1.06182.1938-3.50358.60720.0283-0.15250.06210.0546-0.1495-0.2249-0.19260.38010.1810.0981-0.00010.00930.08810.00280.134947.51043.64268.906
111.3311-0.4494-0.33421.50160.63790.23060.0849-0.0032-0.0408-0.15230.0079-0.037-0.05780.0566-0.09270.1059-0.01760.02520.06850.00750.122138.62221.84236.5095
121.3946-0.06250.18852.1432-0.46461.14760.0388-0.16770.130.0391-0.03380.4362-0.0019-0.1328-0.02590.10990.02680.01490.2758-0.0880.2324.310117.668626.515
131.1714-2.06231.10176.53941.09224.5619-0.2012-0.31370.39120.25610.2506-0.2119-0.41680.1016-0.02430.13930.00240.00810.2385-0.10710.21413.889924.204330.3223
141.39530.2404-0.22211.7784-0.99054.3330.0177-0.00590.242-0.0557-0.0266-0.04-0.1944-0.089-0.02440.17230.03080.00090.0802-0.01270.17520.021322.08096.0296
150.8903-0.08730.23460.8764-0.23092.04740.0119-0.22670.15110.05130.01940.0299-0.1525-0.1361-0.03520.08980.0120.00870.1424-0.03880.129121.473813.345821.3221
161.4862-0.22861.84282.1060.17784.69190.0717-0.2385-0.0238-0.056-0.02480.1753-0.1496-0.4455-0.15570.07130.01280.03390.1943-0.02050.118913.83047.671618.9769
174.688-1.1766-4.83452.22641.44245.00190.12630.14890.6812-0.30150.02240.314-0.6777-0.1253-0.18690.24380.0421-0.07860.23450.02180.34217.785515.4130.0972
184.2195-3.18783.97888.7834-6.51887.9920.0750.24410.1511-0.4293-0.00750.48890.182-0.2589-0.06970.21640.0174-0.05260.2761-0.01650.18647.46416.1533-3.7892
191.3771-0.09410.16361.25820.52172.3421-0.0087-0.15870.0593-0.0013-0.04620.0739-0.0485-0.18460.060.08-0.00060.00830.1339-0.01030.117510.95832.253417.3274
202.0623-0.12060.38273.182-0.86242.09190.1279-0.4191-0.06040.4549-0.20540.20640.1651-0.37820.00280.1977-0.09340.03450.31590.05030.19486.1435-16.824228.3365
210.79220.8742-0.19051.0933-0.97253.10460.2196-0.5472-0.31090.2786-0.2420.07430.3861-0.19360.06960.2264-0.10230.01280.3370.11860.29317.4761-25.750624.5469
224.3984-0.83450.60630.79980.33190.4960.0381-0.159-0.4131-0.1306-0.0436-0.00320.1380.04920.00890.1444-0.0099-0.00520.14660.08460.171631.3223-23.622120.8546
234.2234-2.6525-1.03884.15120.31942.32620.11990.1267-0.6042-0.1197-0.12720.39050.1641-0.2116-0.0010.1302-0.03670.02780.1410.01920.200310.4447-22.69211.7924
241.14540.12410.11360.82050.08851.3083-0.0331-0.2319-0.14820.0007-0.00880.0076-0.0135-0.14560.04190.1021-0.01270.00890.11530.02720.103919.6327-11.562817.5279
254.90480.6958-4.56226.5287-1.43574.47980.0291-0.2781-0.6180.269-0.06140.24550.26080.07820.0620.2035-0.0172-0.00340.27930.05980.166433.2513-16.796134.0049
267.4824-4.77534.56357.3877-2.0655.2836-0.1478-0.45420.42420.66640.0063-0.5084-0.0033-0.21920.11570.1543-0.0319-0.06420.39120.01780.188936.3763-7.689536.6233
274.58931.47682.13831.6880.64142.94450.0683-0.5667-0.22980.177-0.1171-0.03860.0535-0.24890.01240.12-0.00050.02680.24920.02150.121917.3101-4.931530.5466
280.559-0.8168-0.70051.92290.19261.7358-0.0184-0.2074-0.1439-0.00970.01460.0109-0.11-0.1863-0.0260.1049-0.01790.02960.11210.02460.072517.8796-3.093921.4172
292.86861.01670.44294.60230.2993.1453-0.0015-0.01340.034-0.4602-0.0235-0.2742-0.04350.1558-0.00080.15080.03270.06450.1120.01530.142148.7837-15.5354-3.6789
301.80241.126-1.14623.4796-3.62337.7269-0.00440.2522-0.0319-0.6919-0.0488-0.17950.0787-0.14220.00450.39260.04970.0790.14080.00690.180545.997-24.4678-7
311.8696-0.01122.15436.03160.13982.6708-0.02910.0356-0.19610.3330.1846-0.08730.34520.112-0.13120.15050.02470.05540.105-0.00190.116248.2898-25.50635.3335
321.3613-0.13070.35310.69810.07270.86190.00590.0072-0.1114-0.0383-0.0340.00520.03170.0630.02680.12450.0040.02180.0990.01540.116533.735-16.25677.4426
339.6164-1.6037-5.20571.2781-0.11843.817-0.13940.4802-0.5258-0.23010.03080.01390.207-0.23530.13210.4355-0.0557-0.04550.255-0.04920.262321.3914-16.7056-10.28
349.67565.08174.37159.77114.19986.416-0.15110.3003-0.161-0.6456-0.13840.25390.2745-0.46350.31520.34990.0104-0.01010.360.00010.232618.1384-7.7389-11.8888
352.3831-0.19230.23140.74650.01771.3020.01330.1555-0.0205-0.1279-0.0457-0.02410.02310.05530.01910.14370.00290.02390.07840.00750.1336.8078-3.4411-1.404
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 52 )A2 - 52
2X-RAY DIFFRACTION2chain 'A' and (resid 53 through 70 )A53 - 70
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 93 )A71 - 93
4X-RAY DIFFRACTION4chain 'A' and (resid 94 through 120 )A94 - 120
5X-RAY DIFFRACTION5chain 'A' and (resid 121 through 136 )A121 - 136
6X-RAY DIFFRACTION6chain 'A' and (resid 137 through 182 )A137 - 182
7X-RAY DIFFRACTION7chain 'A' and (resid 183 through 196 )A183 - 196
8X-RAY DIFFRACTION8chain 'A' and (resid 197 through 210 )A197 - 210
9X-RAY DIFFRACTION9chain 'A' and (resid 211 through 224 )A211 - 224
10X-RAY DIFFRACTION10chain 'A' and (resid 225 through 244 )A225 - 244
11X-RAY DIFFRACTION11chain 'A' and (resid 245 through 265 )A245 - 265
12X-RAY DIFFRACTION12chain 'B' and (resid 4 through 70 )B4 - 70
13X-RAY DIFFRACTION13chain 'B' and (resid 71 through 93 )B71 - 93
14X-RAY DIFFRACTION14chain 'B' and (resid 94 through 120 )B94 - 120
15X-RAY DIFFRACTION15chain 'B' and (resid 121 through 182 )B121 - 182
16X-RAY DIFFRACTION16chain 'B' and (resid 183 through 196 )B183 - 196
17X-RAY DIFFRACTION17chain 'B' and (resid 197 through 210 )B197 - 210
18X-RAY DIFFRACTION18chain 'B' and (resid 211 through 224 )B211 - 224
19X-RAY DIFFRACTION19chain 'B' and (resid 225 through 265 )B225 - 265
20X-RAY DIFFRACTION20chain 'C' and (resid 2 through 52 )C2 - 52
21X-RAY DIFFRACTION21chain 'C' and (resid 53 through 93 )C53 - 93
22X-RAY DIFFRACTION22chain 'C' and (resid 94 through 120 )C94 - 120
23X-RAY DIFFRACTION23chain 'C' and (resid 121 through 136 )C121 - 136
24X-RAY DIFFRACTION24chain 'C' and (resid 137 through 196 )C137 - 196
25X-RAY DIFFRACTION25chain 'C' and (resid 197 through 210 )C197 - 210
26X-RAY DIFFRACTION26chain 'C' and (resid 211 through 224 )C211 - 224
27X-RAY DIFFRACTION27chain 'C' and (resid 225 through 244 )C225 - 244
28X-RAY DIFFRACTION28chain 'C' and (resid 245 through 265 )C245 - 265
29X-RAY DIFFRACTION29chain 'D' and (resid 2 through 52 )D2 - 52
30X-RAY DIFFRACTION30chain 'D' and (resid 53 through 70 )D53 - 70
31X-RAY DIFFRACTION31chain 'D' and (resid 71 through 93 )D71 - 93
32X-RAY DIFFRACTION32chain 'D' and (resid 94 through 196 )D94 - 196
33X-RAY DIFFRACTION33chain 'D' and (resid 197 through 210 )D197 - 210
34X-RAY DIFFRACTION34chain 'D' and (resid 211 through 224 )D211 - 224
35X-RAY DIFFRACTION35chain 'D' and (resid 225 through 265 )D225 - 265

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