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- PDB-5jy1: Crystal Structure of putative short-chain dehydrogenase/reductase... -

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Basic information

Entry
Database: PDB / ID: 5jy1
TitleCrystal Structure of putative short-chain dehydrogenase/reductase from Burkholderia xenovorans LB400 bound to NAD
ComponentsPutative short-chain dehydrogenase/reductase
KeywordsOXIDOREDUCTASE / dehydrogenase/reductase NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / fatty acid elongation / nucleotide binding
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / 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
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 bound to NAD
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Delker, S.L. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Sep 27, 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: 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)122,72324
Polymers119,1984
Non-polymers3,52520
Water17,835990
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25230 Å2
ΔGint-152 kcal/mol
Surface area31930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.410, 95.700, 84.140
Angle α, β, γ (deg.)90.000, 98.520, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Putative short-chain dehydrogenase/reductase


Mass: 29799.510 Da / Num. of mol.: 4 / Fragment: BuxeA.00010.t.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: Bxe_C0591 / Plasmid: BuxeA.00010.t.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13HF0, 3-oxoacyl-[acyl-carrier-protein] reductase

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Non-polymers , 5 types, 1010 molecules

#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 990 / 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: 2.29 Å3/Da / Density % sol: 46.17 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MCSG-1 h3(270609h3): 30% PEG 3350, 0.2M Lithium Acetate; cryo: 20%EG 2 steps; BuxeA.00010.t.B1.PS37842 at 17.93 mg/ml, puck cnd5-10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 16, 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: 1.65→48.8475 Å / Num. obs: 128505 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.76 % / Biso Wilson estimate: 16.83 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14.47
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.65-1.690.5622.26199.9
1.69-1.740.4482.85199.9
1.74-1.790.3453.7199.9
1.79-1.840.284.491100
1.84-1.910.2295.52199.8
1.91-1.970.1757.22199.9
1.97-2.050.148.91199.9
2.05-2.130.10911.18199.9
2.13-2.220.09213.16199.7
2.22-2.330.07415.861100
2.33-2.460.06617.97199.7
2.46-2.610.05820.071100
2.61-2.790.0523.39199.8
2.79-3.010.04426.351100
3.01-3.30.03729.79199.8
3.3-3.690.03333.72199.8
3.69-4.260.02836.54199.9
4.26-5.220.02538.28199.9
5.22-7.380.02337.53199.8
7.38-48.84750.0238.87196.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2356refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2uvd

2uvd


Resolution: 1.65→48.826 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.66
RfactorNum. reflection% reflection
Rfree0.1749 2040 1.59 %
Rwork0.1462 --
obs0.1467 128477 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.49 Å2 / Biso mean: 23.2 Å2 / Biso min: 9.39 Å2
Refinement stepCycle: final / Resolution: 1.65→48.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8012 0 228 1006 9246
Biso mean--27.61 34.07 -
Num. residues----1064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068737
X-RAY DIFFRACTIONf_angle_d0.80511949
X-RAY DIFFRACTIONf_chiral_restr0.0521318
X-RAY DIFFRACTIONf_plane_restr0.0051561
X-RAY DIFFRACTIONf_dihedral_angle_d15.415186
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6499-1.68830.22241290.21384058534100
1.6883-1.73050.27871340.20284028536100
1.7305-1.77730.23251150.191284438558100
1.7773-1.82960.25451340.177883918525100
1.8296-1.88870.19011300.170184108540100
1.8887-1.95620.21591470.15684388585100
1.9562-2.03450.22151560.156683458501100
2.0345-2.12710.14551390.147684298568100
2.1271-2.23920.17521370.143883958532100
2.2392-2.37950.19251340.141484468580100
2.3795-2.56320.17961500.144284108560100
2.5632-2.82120.18891280.144784608588100
2.8212-3.22930.17131340.14284658599100
3.2293-4.06830.14161360.128284708606100
4.0683-48.84750.13891370.13118528866599
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)
12.00560.3335-0.94141.2448-0.4451.1603-0.22680.1373-0.2426-0.29550.07510.16070.451-0.15830.14190.2611-0.03790.03070.1148-0.00670.216911.4827-9.747421.4553
21.3044-0.7382-0.04520.929-0.08610.6768-0.05570.0132-0.15620.0017-0.02270.15840.1077-0.02390.06890.1143-0.00810.00860.10660.00480.14968.47346.824928.9051
30.8188-0.5912-0.35621.10270.20641.1059-0.00610.1433-0.1733-0.1837-0.07740.28930.1441-0.26920.04750.1331-0.0421-0.03950.1785-0.01840.17987.480511.960213.4893
42.14190.8133-0.98842.12520.41621.8401-0.1697-0.4678-0.0334-0.09840.0991-0.26310.32090.6127-0.05310.2220.05410.04560.2053-0.02060.165940.275810.43963.794
50.16350.0884-0.01231.34691.10651.93680.01760.01950.0075-0.14810.0508-0.1218-0.03970.0836-0.07780.12770.00240.00570.118-0.00440.11630.276724.72437.024
60.33240.0259-0.27911.55830.64691.2682-0.0414-0.1049-0.04250.0350.0604-0.26120.08260.3392-0.08720.120.0065-0.00080.1930.0160.139731.60217.297822.9907
71.3203-0.3661-0.74591.8474-1.13862.7007-0.0225-0.43050.02550.32760.06680.1066-0.08020.3337-0.01060.17810.02870.05020.1955-0.01640.1635-1.090935.898548.4634
81.1048-0.6984-0.1751.3648-0.13230.4444-0.0481-0.0332-0.06020.1320.02720.1901-0.024-0.03420.01850.10750.00860.01240.12380.00430.1390.829222.068437.663
90.7621-0.4706-0.36161.5170.12620.4041-0.0445-0.26390.00250.27750.0638-0.0842-0.00770.1246-0.02650.1524-0.0062-0.01190.18430.00930.110717.343628.608638.3207
100.82960.0783-0.7891.2032-0.36042.3020.08480.06770.2535-0.07290.07950.1555-0.3294-0.1378-0.18560.21730.01920.03370.11850.01130.189515.976556.713419.6819
110.49040.34150.42631.42531.14781.70910.03610.01080.054-0.14050.0051-0.007-0.15380.0375-0.02230.1521-0.00160.00110.12290.00960.114322.075341.173314.2537
120.6655-0.0382-0.3530.95660.33480.72160.07320.12280.0561-0.1906-0.04720.1355-0.1329-0.1635-0.02170.14360.0199-0.02640.13050.01880.115610.720935.722816.3987
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 81 )A1 - 81
2X-RAY DIFFRACTION2chain 'A' and (resid 82 through 177 )A82 - 177
3X-RAY DIFFRACTION3chain 'A' and (resid 178 through 266 )A178 - 266
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 66 )B1 - 66
5X-RAY DIFFRACTION5chain 'B' and (resid 67 through 177 )B67 - 177
6X-RAY DIFFRACTION6chain 'B' and (resid 178 through 266 )B178 - 266
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 66 )C1 - 66
8X-RAY DIFFRACTION8chain 'C' and (resid 67 through 177 )C67 - 177
9X-RAY DIFFRACTION9chain 'C' and (resid 178 through 266 )C178 - 266
10X-RAY DIFFRACTION10chain 'D' and (resid 1 through 81 )D1 - 81
11X-RAY DIFFRACTION11chain 'D' and (resid 82 through 153 )D82 - 153
12X-RAY DIFFRACTION12chain 'D' and (resid 154 through 266 )D154 - 266

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