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- PDB-3u0b: Crystal structure of an oxidoreductase from Mycobacterium smegmatis -

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Basic information

Entry
Database: PDB / ID: 3u0b
TitleCrystal structure of an oxidoreductase from Mycobacterium smegmatis
ComponentsOxidoreductase, short chain dehydrogenase/reductase family protein
KeywordsOXIDOREDUCTASE / Structural Genomics / SSGCID / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
PKS_KR / 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
Oxidoreductase, short chain dehydrogenase/reductase family protein
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsArakaki, T.L. / Staker, B.L. / Clifton, M.C. / Abendroth, J. / Seattle 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
DepositionSep 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Apr 15, 2015Group: Database references
Revision 1.3May 25, 2016Group: Structure summary
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Sep 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 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8662
Polymers46,8431
Non-polymers231
Water10,124562
1
A: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules

A: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7324
Polymers93,6862
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5650 Å2
ΔGint-25 kcal/mol
Surface area28840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.730, 58.220, 76.880
Angle α, β, γ (deg.)90.000, 127.820, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-741-

HOH

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Components

#1: Protein Oxidoreductase, short chain dehydrogenase/reductase family protein /


Mass: 46842.996 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_0372 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0QPE7
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 562 / 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 Å3/Da / Density % sol: 37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MysmA.00010.a at 29.8 mg/ml, 25% PEG 1500, 0.1 M MMT, pH 6.0 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5 Å
DetectorType: Saturn 944+ / Detector: CCD / Date: May 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 39290 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.838 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 28.83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.740.1935.67580275493.6
1.74-1.790.1668.312268276296.9
1.79-1.840.14210.615120273298.7
1.84-1.90.10913.416377267499.7
1.9-1.960.09715.616353259799.6
1.96-2.030.08118.416738252699.6
2.03-2.110.0752217012241699.4
2.11-2.190.06626.119404233399.7
2.19-2.290.06529.619970223099.7
2.29-2.40.0632.620881216199.6
2.4-2.530.05634.520989204399.4
2.53-2.690.05538.221799194499.4
2.69-2.870.05342.323667179799.6
2.87-3.10.04848.224356170899.6
3.1-3.40.04452.722371155699.6
3.4-3.80.04358.420383141999.2
3.8-4.390.04162.818408125999.1
4.39-5.380.04361.615881107399
5.38-7.60.04757.61218783499.3
7.60.04765.1647547297.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.31 Å
Translation2.5 Å47.31 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LLS

3lls


Resolution: 1.7→47.31 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.813 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.162 1975 5 %RANDOM
Rwork0.137 ---
obs0.138 39260 99.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.175 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å2-0.24 Å2
2--0.32 Å20 Å2
3----0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 1 562 3571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223107
X-RAY DIFFRACTIONr_bond_other_d0.0010.022045
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.974238
X-RAY DIFFRACTIONr_angle_other_deg1.57235001
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7215430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70923.689122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.49515485
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5021526
X-RAY DIFFRACTIONr_chiral_restr0.0940.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213586
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02617
X-RAY DIFFRACTIONr_mcbond_it0.4341.52072
X-RAY DIFFRACTIONr_mcbond_other0.0651.5875
X-RAY DIFFRACTIONr_mcangle_it0.82323303
X-RAY DIFFRACTIONr_scbond_it1.78531035
X-RAY DIFFRACTIONr_scangle_it2.8084.5927
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 128 -
Rwork0.189 2613 -
all-2741 -
obs--93.77 %
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)
12.08510.38640.24443.37332.29935.41980.0152-0.08330.01190.07590.0573-0.16420.03860.0888-0.07250.1214-0.00060.00710.12690.01510.13977.621718.8184-25.0717
21.18090.3314-0.24861.6147-1.14681.4677-0.04050.01240.0396-0.0017-0.0342-0.19320.01760.10830.07470.121-0.00020.01430.1211-0.0030.145620.46672.5992-21.7194
30.15280.3894-0.56211.0556-0.78571.08630.0068-0.0592-0.00730.0315-0.0674-0.1353-0.04520.15350.06060.1181-0.006-0.00160.15320.01260.141324.90348.468-11.1322
40.253-0.04850.050.469-0.10950.6596-0.0020.0157-0.0087-0.0015-0.0039-0.01240.01630.02380.00580.12960.00260.00660.14150.00060.141610.84273.0784-11.8893
52.0911-0.0229-0.50291.85860.16651.60390.01750.02180.09180.003-0.0113-0.0014-0.07810.0186-0.00620.1536-0.005-0.01160.14560.01230.1407-9.34618.0776-28.058
60.86840.5088-0.08550.5473-0.10740.93410.0270.03560.09720.0099-0.00980.0568-0.0872-0.0853-0.01730.12570.0118-0.00020.13630.00490.1353-20.39955.8795-29.6687
70.3475-0.1763-0.24990.7060.66821.4041-0.0024-0.03560.03180.0095-0.01330.0471-0.0724-0.08190.01560.13320.0074-0.00450.13860.00330.1394-17.75184.8429-12.9802
80.6814-0.2002-0.23750.04690.04661.02430.0014-0.00440.01650.0201-0.0167-0.0236-0.024-0.03570.01540.1305-0.003-0.00340.14560.00110.1337-9.74385.0524-9.0894
911.9379-2.6614.43614.15585.581332.60430.1619-1.34472.3826-0.621-1.99590.1822-0.937-3.32281.8340.16980.14380.09470.31-0.18860.5265-2.540827.2009-10.7128
100.22380.27660.16010.9346-0.07220.54640.001-0.02480.04530.04910.01430.0187-0.0680.0025-0.01530.1277-0.00220.01220.1428-0.00260.14130.655810.5575-14.4374
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 37
2X-RAY DIFFRACTION2A38 - 69
3X-RAY DIFFRACTION3A70 - 110
4X-RAY DIFFRACTION4A111 - 203
5X-RAY DIFFRACTION5A204 - 242
6X-RAY DIFFRACTION6A243 - 283
7X-RAY DIFFRACTION7A284 - 344
8X-RAY DIFFRACTION8A345 - 390
9X-RAY DIFFRACTION9A391 - 407
10X-RAY DIFFRACTION10A408 - 450

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