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- PDB-3tjr: Crystal structure of a Rv0851c ortholog short chain dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 3tjr
TitleCrystal structure of a Rv0851c ortholog short chain dehydrogenase from Mycobacterium paratuberculosis
Componentsshort chain dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / SCD / NAD / nucleotide adenine dinucleotide / 5-hydroxy NAD / putative uncharacterized protein / asymmetric substrate or cofactor recognition
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
short chain dehydrogenase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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
Unknown ligand / Uncharacterized protein
Similarity search - Component
Biological speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionAug 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 2.0Jan 17, 2018Group: Atomic model / Category: atom_site / Item: _atom_site.type_symbol
Revision 2.1Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: short chain dehydrogenase
B: short chain dehydrogenase


Theoretical massNumber of molelcules
Total (without water)64,1163
Polymers64,1162
Non-polymers01
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-40 kcal/mol
Surface area18890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.110, 130.370, 55.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-537-

HOH

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Components

#1: Protein short chain dehydrogenase


Mass: 32058.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Gene: MAP_0710c / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q742X5, Oxidoreductases
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 2.09 Å3/Da / Density % sol: 41.09 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MypaA.01097.i.A1 PW29443 at 32.8 mg/mL with full tag against JCSG+ screen condition A5: 0.2 M Mg formate, 20% PEG3350, with 15% ethylene glycol as cryo-protectant, crystal tracking ID ...Details: MypaA.01097.i.A1 PW29443 at 32.8 mg/mL with full tag against JCSG+ screen condition A5: 0.2 M Mg formate, 20% PEG3350, with 15% ethylene glycol as cryo-protectant, crystal tracking ID 222227a5, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979175 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 1, 2011
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979175 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 71659 / Num. obs: 70936 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 19.407 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 27.39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.6-1.643.50.1318.22181035222521399.8
1.64-1.690.129.7719898513999.8
1.69-1.740.10411.2319234493599.8
1.74-1.790.08713.2818677479199.7
1.79-1.850.07415.4318381469499.9
1.85-1.910.06118.7717595451099.8
1.91-1.980.05321.4317027436499.7
1.98-2.070.04425.4616449419899.6
2.07-2.160.03928.9315724403599.4
2.16-2.260.03532.0814940384699.5
2.26-2.390.03234.2614316368699.1
2.39-2.530.033713387343998.5
2.53-2.70.02740.0112593325898.8
2.7-2.920.02542.5911662302897.9
2.92-3.20.02346.5210793281498.5
3.2-3.580.02251.189570252597.5
3.58-4.130.0254.348368223697
4.13-5.060.01757.37235190796.3
5.06-7.160.01755.725813149996.3
7.160.01755.74277381989.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å48.95 Å
Translation3 Å48.95 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
EPICS-baseddata acquisition systemdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IOY

3ioy


Resolution: 1.6→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.1801 / WRfactor Rwork: 0.1607 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.903 / SU B: 2.424 / SU ML: 0.045 / SU R Cruickshank DPI: 0.0824 / SU Rfree: 0.0791 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.082 / ESU R Free: 0.079 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.1858 3590 5.1 %RANDOM
Rwork0.1651 ---
obs0.1662 70935 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 47.02 Å2 / Biso mean: 13.3916 Å2 / Biso min: 5.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20 Å2
2---0.27 Å20 Å2
3---0.68 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3870 0 45 552 4467
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194102
X-RAY DIFFRACTIONr_angle_refined_deg1.6031.9615603
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2945547
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50622.35183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.3515618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3131544
X-RAY DIFFRACTIONr_chiral_restr0.2780.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213171
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 271 -
Rwork0.199 4621 -
all-4892 -
obs--99.78 %
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)
111.8312-5.2952.08676.5936-2.17530.7334-0.3544-0.19640.2130.46550.1442-0.7557-0.1588-0.05540.21020.1315-0.0123-0.0410.0113-0.0130.137810.974952.999416.0438
20.4161-0.25220.24860.3222-0.00010.3819-0.00880.0010.0255-0.0101-0.0186-0.0012-0.0069-0.02970.02730.0536-0.0006-0.0050.04660.00590.05580.903844.92444.2363
30.2767-0.04830.12450.7115-0.01310.0588-0.00570.00150.0203-0.00870.00810.0283-0.00150.0005-0.00240.0448-0.00830.00160.05160.00280.05289.537131.436610.8295
40.4836-0.44260.19820.5195-0.16870.222-0.0059-0.0484-0.01530.07060.02390.0297-0.0007-0.0239-0.0180.0460.00770.00350.06960.00370.03229.503327.573423.8725
50.5782-0.6271-0.07081.0045-0.13760.15440.01660.015-0.0114-0.0292-0.0201-0.010.01340.00680.00350.0493-0.0031-0.0020.0341-0.01470.069922.69890.47666.2813
60.22940.1223-0.08860.5556-0.0670.09520.0147-0.0069-0.0238-0.0051-0.0137-0.0166-0.003-0.0021-0.0010.0455-0.00250.0020.0535-0.00190.055616.835816.529811.2189
76.7060.6049-1.62310.2348-0.8443.10250.2603-0.28660.4452-0.0187-0.09470.0590.11710.3359-0.16570.0816-0.06370.01930.1246-0.03970.043543.333132.040812.7948
80.3533-0.3141-0.01180.44-0.01410.1634-0.0169-0.0419-0.00390.08270.0142-0.04240.00590.00830.00270.04980.0072-0.0120.0642-0.01630.036321.282721.870924.5749
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 11
2X-RAY DIFFRACTION2A12 - 86
3X-RAY DIFFRACTION3A87 - 196
4X-RAY DIFFRACTION4A197 - 280
5X-RAY DIFFRACTION5B4 - 96
6X-RAY DIFFRACTION6B97 - 193
7X-RAY DIFFRACTION7B194 - 219
8X-RAY DIFFRACTION8B220 - 280

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