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- PDB-1y0h: Structure of Rv0793 from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 1y0h
TitleStructure of Rv0793 from Mycobacterium tuberculosis
Componentshypothetical protein Rv0793
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / ferredoxin-like fold / alpha+beta sandwich with antiparallel beta-sheet / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


Oxidoreductases / catalytic activity / monooxygenase activity
Similarity search - Function
ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Putative monooxygenase Rv0793
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsLemieux, M.J. / Ference, C. / Cherney, M.M. / Wang, M. / Garen, C. / James, M.N. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2005
Title: The crystal structure of Rv0793, a hypothetical monooxygenase from M. tuberculosis
Authors: Lemieux, M.J. / Ference, C. / Cherney, M.M. / Wang, M. / Garen, C. / James, M.N.
History
DepositionNov 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: hypothetical protein Rv0793
B: hypothetical protein Rv0793
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7035
Polymers22,5262
Non-polymers1773
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-13 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.440, 34.600, 42.850
Angle α, β, γ (deg.)103.44, 107.96, 94.34
Int Tables number1
Space group name H-MP1

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Components

#1: Protein hypothetical protein Rv0793


Mass: 11262.771 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv0793 / Plasmid: pDEST15 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: O86332
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 1.84 Å3/Da / Density % sol: 33.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG20K, hepes, ammonium acetate, ethylene glycol, isopropanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.979232 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 13, 2003
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979232 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 20461 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Χ2: 1.059 / Net I/σ(I): 8.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.485 / Mean I/σ(I) obs: 4.8 / Num. unique all: 2027 / Rsym value: 0.48 / Χ2: 1.031 / % possible all: 95.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
REFMACrefinement
MOSFLMdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.6→29.59 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.978 / SU ML: 0.071 / SU R Cruickshank DPI: 0.114 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.114 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 994 5.1 %RANDOM
Rwork0.173 ---
all0.176 ---
obs0.202 19610 93.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.607 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.06 Å20.07 Å2
2--0.08 Å2-0.04 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1549 0 12 208 1769
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONr_bond_refined_d0.00816110.022
X-RAY DIFFRACTIONr_angle_refined_deg1.21921821.995
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.171975
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.0087920.886
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.44926215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7732715
X-RAY DIFFRACTIONr_chiral_restr0.0792410.2
X-RAY DIFFRACTIONr_gen_planes_refined0.00412590.02
X-RAY DIFFRACTIONr_nbd_refined0.1987720.2
X-RAY DIFFRACTIONr_nbtor_refined0.30710870.2
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1311630.2
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.176460.2
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.139360.2
X-RAY DIFFRACTIONr_mcbond_it0.6210291.5
X-RAY DIFFRACTIONr_mcangle_it1.04916072
X-RAY DIFFRACTIONr_scbond_it2.0276433
X-RAY DIFFRACTIONr_scangle_it3.0335754.5
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 56 -
Rwork0.193 1229 -
obs-7385 82.53 %
Refinement TLS params.Method: refined / Origin x: -2.182 Å / Origin y: 6.56 Å / Origin z: 16.212 Å
111213212223313233
T-0.0273 Å20.0029 Å2-0.0172 Å2--0.021 Å20.0113 Å2---0.0052 Å2
L0.2516 °2-0.0005 °2-0.3001 °2-0.52 °20.2879 °2--0.8915 °2
S-0.0083 Å °-0.0786 Å °-0.019 Å °0.0037 Å °0.021 Å °-0.0215 Å °0.0358 Å °0.0874 Å °-0.0126 Å °
Refinement TLS groupSelection: ALL

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