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- PDB-5uzx: Crystal Structure of Putative short-chain dehydrogenase/reductase... -

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Basic information

Entry
Database: PDB / ID: 5uzx
TitleCrystal Structure of Putative short-chain dehydrogenase/reductase from Burkholderia multivorans with bound NADP
ComponentsPutative short-chain alcohol dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase/reductase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Short-chain alcohol dehydrogenase
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Putative short-chain dehydrogenase/reductase from Burkholderia multivorans with bound NADP
Authors: Delker, S.L. / Mayclin, S.J. / Lorimer, D. / Edwards, T.E.
History
DepositionFeb 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 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: Putative short-chain alcohol dehydrogenase
B: Putative short-chain alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,93420
Polymers53,5272
Non-polymers2,40718
Water8,071448
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative short-chain alcohol dehydrogenase
hetero molecules

B: Putative short-chain alcohol dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,93420
Polymers53,5272
Non-polymers2,40718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Buried area8680 Å2
ΔGint-59 kcal/mol
Surface area17580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.400, 76.150, 65.480
Angle α, β, γ (deg.)90.000, 109.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative short-chain alcohol dehydrogenase / BumuA.00010.z.B1


Mass: 26763.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (strain ATCC 17616 / 249) (bacteria)
Gene: BMULJ_04988 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KNM5

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Non-polymers , 5 types, 466 molecules

#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#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.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 448 / 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: 2.03 Å3/Da / Density % sol: 39.49 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MCSG-1 F10(287571F10): 0.1 M Tris HCl, pH 8.5, 2 M Ammonium Sulfate, cryo: 25% Ethylene Glycol +5mM NADP: BumuA.00010.z.B1.PS37887at 20 mg/ml, puck wdq6-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 15, 2017 / 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: 1.5→43.195 Å / Num. obs: 67944 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.071 % / Biso Wilson estimate: 18.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.054 / Χ2: 1.018 / Net I/σ(I): 14.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.543.2920.5562.0148150.7790.66295.2
1.54-1.583.9290.4462.8648540.8510.51699.2
1.58-1.634.160.3723.647850.9110.42699.7
1.63-1.684.1540.2964.4746710.940.33999.6
1.68-1.734.1690.2365.5644840.960.2799.6
1.73-1.794.1750.1847.1243340.9750.2199.7
1.79-1.864.1770.149.0642110.9850.16199.6
1.86-1.944.1750.10411.8240660.9910.11999.7
1.94-2.024.1790.08414.5138560.9940.09699.7
2.02-2.124.170.06718.0737080.9950.07799.5
2.12-2.244.1570.05820.7435250.9970.06699.5
2.24-2.374.1410.05123.6233170.9970.05899.3
2.37-2.544.1340.04725.5231180.9970.05399.2
2.54-2.744.0920.04527.7229360.9970.05198.9
2.74-34.1060.04130.0526630.9970.04798.8
3-3.354.0940.03832.4324260.9980.04398.8
3.35-3.874.1080.03534.3421720.9970.04198.8
3.87-4.744.1040.03135.0617980.9980.03699.1
4.74-6.714.1010.02935.0314330.9980.03399.4
6.71-43.1953.9830.02734.817720.9980.03196.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2666refinement
PDB_EXTRACT3.22data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5tt1

5tt1


Resolution: 1.5→43.195 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.5
RfactorNum. reflection% reflection
Rfree0.1991 1948 2.87 %
Rwork0.1646 --
obs0.1656 67939 99.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.46 Å2 / Biso mean: 25.499 Å2 / Biso min: 12.63 Å2
Refinement stepCycle: final / Resolution: 1.5→43.195 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3471 0 157 456 4084
Biso mean--29.8 35.6 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053780
X-RAY DIFFRACTIONf_angle_d0.8665149
X-RAY DIFFRACTIONf_chiral_restr0.076591
X-RAY DIFFRACTIONf_plane_restr0.006703
X-RAY DIFFRACTIONf_dihedral_angle_d19.3661464
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4999-1.53740.2791460.23574490463695
1.5374-1.5790.24011460.21294648479499
1.579-1.62550.20521240.189847614885100
1.6255-1.67790.22861240.18647574881100
1.6779-1.73790.24951500.181847034853100
1.7379-1.80750.20871130.172247264839100
1.8075-1.88980.19871250.170347654890100
1.8898-1.98940.20521350.169847454880100
1.9894-2.1140.21411390.164647324871100
2.114-2.27730.19071780.163546834861100
2.2773-2.50640.20751270.16124724485199
2.5064-2.8690.20481280.16464765489399
2.869-3.61440.22681700.15754700487099
3.6144-43.21310.15571430.15324792493599
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)
13.59751.4551-0.15383.8309-0.95591.29710.00830.22980.1757-0.17750.05020.1717-0.1456-0.1277-0.05760.20040.0329-0.01590.1738-0.00730.1207-7.64194.295416.4529
21.0377-0.2163-0.71170.47640.553.70790.02650.0841-0.0492-0.0557-0.0405-0.0042-0.0616-0.1960.01550.14660.00330.00060.14140.0090.154-5.595-1.765930.0808
31.11660.2081-0.22940.4385-0.14573.1360.03080.07290.1785-0.0934-0.0372-0.063-0.28240.1737-0.02140.1446-0.00950.01060.15560.00720.16585.95162.141631.2192
44.47290.89880.70494.88690.59793.7466-0.0226-0.3245-0.19840.24290.0519-0.11110.11240.0478-0.01660.14730.03190.00840.16970.01310.083421.9278-13.84036.9591
52.6989-1.99820.13917.7929-2.08534.3591-0.0704-0.1294-0.18110.20270.19240.2740.1613-0.2269-0.12210.0771-0.02540.02090.17410.00070.12510.6681-11.98214.9123
60.71-0.014-0.03990.9865-0.02882.4204-0.021-0.02330.02710.04440.0367-0.03660.1525-0.0086-0.01270.12180.00240.00160.13150.00010.133420.247-6.7811-11.0374
71.5139-0.7844-0.71413.5382-0.44142.7554-0.1236-0.0292-0.08780.02670.0309-0.15390.36970.1820.06390.12660.0372-0.01080.1963-0.02060.160931.0916-11.9107-4.8208
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 7 through 78 )A7 - 78
2X-RAY DIFFRACTION2chain 'A' and (resid 79 through 141 )A79 - 141
3X-RAY DIFFRACTION3chain 'A' and (resid 142 through 237 )A142 - 237
4X-RAY DIFFRACTION4chain 'B' and (resid 7 through 39 )B7 - 39
5X-RAY DIFFRACTION5chain 'B' and (resid 40 through 78 )B40 - 78
6X-RAY DIFFRACTION6chain 'B' and (resid 79 through 177 )B79 - 177
7X-RAY DIFFRACTION7chain 'B' and (resid 178 through 237 )B178 - 237

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