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- PDB-3qha: Crystal structure of a Putative oxidoreductase from Mycobacterium... -

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Basic information

Entry
Database: PDB / ID: 3qha
TitleCrystal structure of a Putative oxidoreductase from Mycobacterium avium 104
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Mycobacterium avium 104 / rossmann fold / Putative oxidoreductase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors / NAD binding / NADP binding / oxidoreductase activity
Similarity search - Function
3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...3-hydroxyisobutyrate dehydrogenase-related, conserved site / 3-hydroxyisobutyrate dehydrogenase signature. / 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain / NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase / 3-hydroxyisobutyrate dehydrogenase-related / 6-phosphogluconate dehydrogenase, NADP-binding / NAD binding domain of 6-phosphogluconate dehydrogenase / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative oxidoreductase / Putative oxidoreductase
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 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
DepositionJan 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 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: Putative oxidoreductase
B: Putative oxidoreductase


Theoretical massNumber of molelcules
Total (without water)61,8452
Polymers61,8452
Non-polymers00
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-86 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.055, 76.829, 115.879
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative oxidoreductase /


Mass: 30922.332 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Strain: 104 / Gene: A0QAQ2_MYCA1, MAV_0715 / Plasmid: AVA0241 / Production host: Escherichia coli (E. coli)
References: UniProt: A0QAQ2, UniProt: A0A0H2ZSR3*PLUS, Oxidoreductases; Acting on the CH-OH group of donors
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.41 Å3/Da / Density % sol: 49.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: MyavA.01379.a.A1 22.39 mg/ml, 20% PEG 6000, 0.1 M Hepes pH 7.0, 0.2M CaCl2, cryo-protectant 25% Ethylene glycol, 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: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Single crystal, cylindrically bent, Si (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 29158 / % possible obs: 100 % / Redundancy: 7.2 % / Rmerge(I) obs: 0.105 / Χ2: 0.962 / Net I/σ(I): 7.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.25-2.327.30.64924151.0541100
2.32-2.397.30.51123730.8651100
2.39-2.487.30.4124020.8921100
2.48-2.587.30.32624080.8681100
2.58-2.697.30.27823670.9841100
2.69-2.837.30.22124140.9531100
2.83-3.017.30.15723841.0091100
3.01-3.247.30.11224111.071100
3.24-3.577.20.09124441.0011100
3.57-4.097.20.08524540.9771100
4.09-5.1570.05724820.9611100
5.15-506.80.03326040.9121100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 59.57 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å46.31 Å
Translation2.5 Å46.31 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VPD

1vpd


Resolution: 2.25→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2113 / WRfactor Rwork: 0.1865 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8474 / SU B: 13.166 / SU ML: 0.147 / SU R Cruickshank DPI: 0.2912 / SU Rfree: 0.2108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 1475 5.1 %RANDOM
Rwork0.1995 ---
obs0.2013 28979 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.11 Å2 / Biso mean: 28.4089 Å2 / Biso min: 7.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---1.22 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 2.25→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3968 0 0 284 4252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0214036
X-RAY DIFFRACTIONr_bond_other_d0.0010.022535
X-RAY DIFFRACTIONr_angle_refined_deg0.9161.9685509
X-RAY DIFFRACTIONr_angle_other_deg0.84136213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.345553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03623.562146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20615588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5981526
X-RAY DIFFRACTIONr_chiral_restr0.0530.2662
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214637
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02777
X-RAY DIFFRACTIONr_mcbond_it0.2241.52741
X-RAY DIFFRACTIONr_mcbond_other0.0261.51140
X-RAY DIFFRACTIONr_mcangle_it0.42824319
X-RAY DIFFRACTIONr_scbond_it0.59831295
X-RAY DIFFRACTIONr_scangle_it1.0424.51190
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 117 -
Rwork0.267 2009 -
all-2126 -
obs--98.75 %
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)
13.6575-0.1554-0.90731.05320.20052.46360.1879-0.37640.47040.1119-0.0554-0.0215-0.3310.2163-0.13250.0654-0.04690.02230.0534-0.04260.085915.954-8.5161-2.6145
21.3999-0.06840.39280.9218-0.07632.01260.0286-0.0474-0.10210.07320.01310.01940.02660.0883-0.04160.05120.0126-0.0050.0530.00430.079312.9417-19.7485-9.3599
30.6731-0.20650.21290.8917-0.31690.5655-0.00710.0183-0.0138-0.19130.0456-0.09360.06590.0027-0.03860.0951-0.01240.00040.073-0.02760.06133.4892-17.276-38.9782
41.96210.45820.10872.53880.14931.4888-0.0380.0954-0.0425-0.25260.00210.23270.0129-0.1260.03580.0920.0094-0.050.0539-0.01220.056-20.9097-14.5486-46.3009
50.4439-0.27130.17441.033-0.21190.5279-0.0402-0.01040.0338-0.01140.0315-0.1469-0.01960.06870.00870.0458-0.006-0.00150.0643-0.02190.06989.8027-9.5768-30.712
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 112
2X-RAY DIFFRACTION2A113 - 180
3X-RAY DIFFRACTION3A181 - 287
4X-RAY DIFFRACTION4B11 - 169
5X-RAY DIFFRACTION5B170 - 288

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