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- PDB-6ujk: Crystal Structure of a Probable short-chain type dehydrogenase/re... -

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Basic information

Entry
Database: PDB / ID: 6ujk
TitleCrystal Structure of a Probable short-chain type dehydrogenase/reductase (Rv1144) from Mycobacterium tuberculosis with bound NAD
ComponentsUncharacterized oxidoreductase Rv1144
KeywordsOXIDOREDUCTASE / SSGCID / dehydrogenase / reductase / NAD / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Oxidoreductases / peptidoglycan-based cell wall / oxidoreductase activity / plasma membrane
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Uncharacterized oxidoreductase Rv1144
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Probable short-chain type dehydrogenase/reductase (Rv1144) from Mycobacterium tuberculosis with bound NAD
Authors: Dranow, D.M. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionOct 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 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: Uncharacterized oxidoreductase Rv1144
B: Uncharacterized oxidoreductase Rv1144
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,57512
Polymers53,6922
Non-polymers1,88310
Water9,350519
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-19 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.880, 124.070, 95.620
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-417-

HOH

21A-541-

HOH

31A-680-

HOH

41B-584-

HOH

51B-633-

HOH

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Components

#1: Protein Uncharacterized oxidoreductase Rv1144 / MytuD.00554.a.B1


Mass: 26845.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: Rv1144 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WGQ7, Oxidoreductases
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: MytuD.00554.a.B1.PW38579 at 23.33 mg/ml was incubated with 5 mM NAD, then was mixed 1:1 with MCSG1 (d9): 25% (w/v) PEG-3350, 0.1 M Tris:HCl, pH = 8.5, 0.2 M NaCl, 20% ethylene glycol cro. ...Details: MytuD.00554.a.B1.PW38579 at 23.33 mg/ml was incubated with 5 mM NAD, then was mixed 1:1 with MCSG1 (d9): 25% (w/v) PEG-3350, 0.1 M Tris:HCl, pH = 8.5, 0.2 M NaCl, 20% ethylene glycol cro. Tray: 307357d9, puck: ukh4-4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.2→29.96 Å / Num. obs: 141537 / % possible obs: 99.6 % / Redundancy: 6.175 % / Biso Wilson estimate: 15.064 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.047 / Χ2: 1.048 / Net I/σ(I): 23.01 / Num. measured all: 873969 / Scaling rejects: 2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.2-1.234.120.1727.07411421042299850.970.19895.8
1.23-1.265.5210.1599.185602310183101470.9820.17699.6
1.26-1.36.5340.14211.5264465986798660.9890.154100
1.3-1.346.4890.12612.7262158957995790.9920.137100
1.34-1.396.2490.11513.658326933493330.9920.126100
1.39-1.436.4470.10215.4758194902890270.9930.112100
1.43-1.496.680.08618.4758317873287300.9960.093100
1.49-1.556.5270.07421.3954650837383730.9960.08100
1.55-1.626.2450.06723.2950283805580520.9960.073100
1.62-1.76.3870.05926.1449346772777260.9970.065100
1.7-1.796.6070.05429.2148255730473040.9970.058100
1.79-1.96.4740.04832.2545028695769550.9980.052100
1.9-2.036.1130.04434.4140026656365480.9980.04899.8
2.03-2.196.2820.04137.1838275610160930.9980.04599.9
2.19-2.46.4770.03939.2836317561056070.9980.04299.9
2.4-2.686.2820.03839.7832038510951000.9990.04199.8
2.68-3.15.8760.03739.5826529453045150.9980.04199.7
3.1-3.796.5270.03543.3325102385238460.9990.03899.8
3.79-5.376.1540.03342.8218542301730130.9990.03699.9
5.37-29.966.3020.03243.0710953175017380.9990.03499.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.17rc1_3602refinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PYM

3pym


Resolution: 1.2→29.96 Å / SU ML: 0.07 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 11.11
RfactorNum. reflection% reflectionSelection details
Rfree0.1365 1873 1.32 %Random
Rwork0.1222 ---
obs0.1224 141531 99.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 64.64 Å2 / Biso mean: 15.5475 Å2 / Biso min: 6.03 Å2
Refinement stepCycle: final / Resolution: 1.2→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3512 0 144 535 4191
Biso mean--16.37 29.08 -
Num. residues----489
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.2-1.230.12781540.1033102061036096
1.23-1.270.13871170.09811069010807100
1.27-1.310.1361440.09581071610860100
1.31-1.360.12531360.09561070510841100
1.36-1.410.12391250.09671074510870100
1.41-1.470.11311360.09571074110877100
1.47-1.550.10251300.09331075410884100
1.55-1.650.11521530.10231072510878100
1.65-1.780.131600.11461077710937100
1.78-1.960.13411690.12431073810907100
1.96-2.240.12781190.12681084710966100
2.24-2.820.15441830.14141084111024100
2.82-29.960.14831470.13911117311320100

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