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- PDB-6uh2: Crystal Structure of Short Chain Dehydrogenase from Leptospira bo... -

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Basic information

Entry
Database: PDB / ID: 6uh2
TitleCrystal Structure of Short Chain Dehydrogenase from Leptospira borgpetersenii serovar Hardjo-bovis (Strain JB197) with bound NAD+
ComponentsShort chain dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / SHORT CHAIN DEHYDROGENASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyEnoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Short chain dehydrogenase
Function and homology information
Biological speciesLeptospira borgpetersenii serovar Hardjo-bovis
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)HHSN272201700059C United States
CitationJournal: TO BE PUBLISHED
Title: TBD
Authors: Davies, D.R. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E. / Horanyi, P.S.
History
DepositionSep 26, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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

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Assembly

Deposited unit
A: Short chain dehydrogenase
B: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3504
Polymers59,0232
Non-polymers1,3272
Water7,746430
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-40 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.360, 131.260, 120.420
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-480-

HOH

21B-556-

HOH

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Components

#1: Protein Short chain dehydrogenase / LPBOA.00010.A.B1


Mass: 29511.389 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptospira borgpetersenii serovar Hardjo-bovis (strain JB197) (bacteria)
Strain: JB197 / Gene: LBJ_1131 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q04TM7
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MORPHEUS D8 (100 MM HEPES/MOPS, PH 7.5, 0.02 M each 1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol, 12.5% MPD, 12.5% PEG 1000, 12.5% PEG3350), 5 mM NAD+ soak

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 39676 / % possible obs: 99.3 % / Redundancy: 6.08 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 21.63
Reflection shellResolution: 1.9→1.95 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 2772 / % possible all: 95.4

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Processing

Software
NameVersionClassification
PHENIXdev_3584refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GWR

5gwr


Resolution: 1.9→36.003 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.51
RfactorNum. reflection% reflection
Rfree0.1914 2114 5.33 %
Rwork0.1552 --
obs0.1571 39673 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 97.09 Å2 / Biso mean: 25.4597 Å2 / Biso min: 6.91 Å2
Refinement stepCycle: final / Resolution: 1.9→36.003 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3969 0 88 430 4487
Biso mean--20.95 35.27 -
Num. residues----509
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9-1.94410.27981490.238234095
1.9441-1.99280.21171260.1913244597
1.9928-2.04660.23121310.1731245198
2.0466-2.10690.20721290.15632484100
2.1069-2.17480.2151320.15522500100
2.1748-2.25260.21121480.16092496100
2.2526-2.34270.20821640.15742488100
2.3427-2.44930.23191620.15932477100
2.4493-2.57840.21091570.15752476100
2.5784-2.73990.18961260.16262544100
2.7399-2.95140.23011350.15922519100
2.9514-3.24820.19411340.15672535100
3.2482-3.71780.13941410.13332558100
3.7178-4.68250.14511290.12452570100
4.6825-36.0030.18351510.16712676100
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)
10.4359-0.3928-0.11590.39350.16130.0863-0.0617-0.46040.67250.1350.3626-0.2-0.4472-0.0338-0.26140.53560.14340.06330.4484-0.09620.5139-30.370239.4567.7582
21.0910.15330.3851.23020.18851.00840.0193-0.195-0.21570.25170.0276-0.17120.26550.092-0.04190.21410.0322-0.00340.17670.06680.2041-24.154310.9877-6.4637
30.43150.0022-0.32510.54290.33761.9691-0.0069-0.0551-0.13010.0544-0.0064-0.04290.13630.1233-0.00450.13740.01310.01390.11720.02410.1708-29.526611.5325-20.205
40.3864-0.28080.25191.41640.17861.61870.0212-0.01520.0462-0.08870.0438-0.143-0.03130.1826-0.02840.0974-0.00770.00630.1119-0.00320.1439-29.05221.7861-23.8415
50.67780.39410.13141.653-0.28641.239-0.04280.297-0.1397-0.1817-0.0402-0.40240.08290.37280.09720.13430.02170.03410.26570.01650.2056-16.659227.0795-18.8527
61.8716-0.42980.08071.43970.19770.3467-0.03040.0207-0.0238-0.05770.0078-0.0533-0.02260.08650.00450.13830.008-0.01810.1073-0.00510.1338-27.922731.8448-16.5514
72.7599-0.8842-1.52920.80650.49360.9927-0.2252-0.4166-0.45610.51480.0530.71550.1727-0.46630.02710.39220.02890.05120.47240.00780.5115-28.793842.4526.0314
80.3574-0.04330.24040.33590.01981.6933-0.084-0.06490.10470.1527-0.04390.0004-0.4060.05760.07860.2184-0.0228-0.03860.1127-0.00110.1398-27.440256.1825-9.4657
91.0257-0.30130.4231.7697-0.08491.955-0.0163-0.02720.00480.0226-0.04850.085-0.20820.00350.05410.1218-0.0111-0.00620.08720.00510.0603-28.360250.1572-22.9539
101.79320.1487-0.20651.6946-0.25721.27580.0540.05320.06770.0522-0.01520.2736-0.1405-0.1716-0.02760.12460.0193-0.01220.11940.0030.1322-35.553538.9636-13.773
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -5 through 10 )A-5 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 78 )A11 - 78
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 131 )A79 - 131
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 186 )A132 - 186
5X-RAY DIFFRACTION5chain 'A' and (resid 187 through 233 )A187 - 233
6X-RAY DIFFRACTION6chain 'A' and (resid 234 through 253 )A234 - 253
7X-RAY DIFFRACTION7chain 'B' and (resid -6 through 10 )B-6 - 10
8X-RAY DIFFRACTION8chain 'B' and (resid 11 through 102 )B11 - 102
9X-RAY DIFFRACTION9chain 'B' and (resid 103 through 186 )B103 - 186
10X-RAY DIFFRACTION10chain 'B' and (resid 187 through 253 )B187 - 253

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