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- PDB-3tsc: Crystal structure of short chain dehydrogenase MAP_2410 from Myco... -

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Basic information

Entry
Database: PDB / ID: 3tsc
TitleCrystal structure of short chain dehydrogenase MAP_2410 from Mycobacterium paratuberculosis bound to NAD
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / nucleotide / adenine dinucleotide / short chain dehydrogenase / SRD family protein / carveol dehydrogenase / ortholog
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
Mycofactocin-dependent oxidoreductase / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Uncharacterized protein
Similarity search - Component
Biological speciesMycobacterium avium subsp. paratuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: Sci Rep / Year: 2017
Title: Mycofactocin-associated mycobacterial dehydrogenases with non-exchangeable NAD cofactors.
Authors: Haft, D.H. / Pierce, P.G. / Mayclin, S.J. / Sullivan, A. / Gardberg, A.S. / Abendroth, J. / Begley, D.W. / Phan, I.Q. / Staker, B.L. / Myler, P.J. / Marathias, V.M. / Lorimer, D.D. / Edwards, T.E.
#1: Journal: 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
DepositionSep 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative oxidoreductase
B: Putative oxidoreductase
C: Putative oxidoreductase
D: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,42210
Polymers116,5324
Non-polymers2,8906
Water11,494638
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19590 Å2
ΔGint-146 kcal/mol
Surface area31350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.980, 127.170, 69.690
Angle α, β, γ (deg.)90.000, 104.490, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative oxidoreductase


Mass: 29133.008 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium subsp. paratuberculosis (bacteria)
Gene: MAP_2410 / Production host: Escherichia coli (E. coli) / References: UniProt: Q73X99
#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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / 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: 2.13 Å3/Da / Density % sol: 42.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: MypaA.01326.g.A1 PW29476 at 27.6 mg/mL against JCSG+ D5, 70% MPD, 0.1 M Hepes pH 7.5, crystal tracking ID 220650d3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 61220 / Num. obs: 60295 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 21.616 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.54
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.05-2.10.4743.2117243436497.3
2.1-2.160.4073.8818289432398.4
2.16-2.220.3684.2717882421998.3
2.22-2.290.3095.0216676405497.7
2.29-2.370.2745.6116833396598.5
2.37-2.450.2496.2116443384798.4
2.45-2.540.2266.7715938373998.7
2.54-2.650.2067.3715242356398.6
2.65-2.760.1748.6514512344198.8
2.76-2.90.1469.914094332299.2
2.9-3.060.11512.2113185310498.9
3.06-3.240.09314.4112489294899.3
3.24-3.470.07816.5511807280999.2
3.47-3.740.06718.9310846260199
3.74-4.10.05721.329940239299
4.1-4.580.05123.79081216899.3
4.58-5.290.05322.577906191999.1
5.29-6.480.06620.136672161898.9
6.48-9.170.04826.045240125499.1
9.170.0429.58257864589.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.94 Å
Translation3 Å19.94 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3pgx

3pgx


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.1844 / WRfactor Rwork: 0.141 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8636 / SU B: 8.124 / SU ML: 0.117 / SU R Cruickshank DPI: 0.2164 / SU Rfree: 0.1751 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2125 3045 5.1 %RANDOM
Rwork0.1623 ---
obs0.1648 60294 98.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 43.82 Å2 / Biso mean: 14.8272 Å2 / Biso min: 4.63 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å20.98 Å2
2---1.51 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7990 0 192 638 8820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0198380
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.97911474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.19751090
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29923.887337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.733151244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3931565
X-RAY DIFFRACTIONr_chiral_restr0.090.21333
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216381
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 214 -
Rwork0.243 4073 -
all-4287 -
obs--97.32 %
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)
10.1235-0.0885-0.04430.1391-0.01580.2809-0.02530.0229-0.00310.0301-0.00160.01420.0308-0.01290.02690.0138-0.0016-0.0030.03140.00220.0366-18.01612.9861-3.8897
20.11920.1279-0.04180.1978-0.08380.33460.02130.0018-0.0101-0.01230.0041-0.012-0.0536-0.0404-0.02550.03890.00950.00540.02610.00460.0208-10.124635.1775-39.1574
30.1546-0.1132-0.07620.144-0.04050.34570.0527-0.0115-0.007-0.00030.0085-0.0014-0.11140.0266-0.06120.0478-0.01220.00730.0138-0.01230.0381-10.408141.5987-7.616
40.17140.0376-0.02390.09210.00230.23720.0024-0.0230.0046-0.0323-0.0184-0.01630.03810.00710.0160.02270.00610.00130.0290.00140.036-2.78187.314-31.4902
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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