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- PDB-4qvb: Mycobacterium tuberculosis protein Rv1155 in complex with co-enzy... -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4qvb
TitleMycobacterium tuberculosis protein Rv1155 in complex with co-enzyme F420
ComponentsRv1155 protein
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


vitamin B6 metabolic process / coenzyme F420 binding / oxidoreductase activity, acting on the CH-CH group of donors / Oxidoreductases / pyridoxal phosphate binding / FMN binding / protein homodimerization activity
Similarity search - Function
: / F420-binding domain, putative / Pyridoxamine 5'-phosphate oxidase, putative / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta
Similarity search - Domain/homology
COENZYME F420 / FORMIC ACID / 1,3-PROPANDIOL / S-1,2-PROPANEDIOL / : / F420H(2)-dependent reductase Rv1155
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMashalidis, E.H. / Gittis, A.G. / Tomczak, A. / Abell, C. / Barry III, C.E. / Garboczi, D.N.
CitationJournal: Protein Sci. / Year: 2015
Title: Molecular insights into the binding of coenzyme F420 to the conserved protein Rv1155 from Mycobacterium tuberculosis.
Authors: Mashalidis, E.H. / Gittis, A.G. / Tomczak, A. / Abell, C. / Barry, C.E. / Garboczi, D.N.
History
DepositionJul 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 25, 2015Provider: repository / Type: Initial release
Revision 1.1May 20, 2015Group: Database references
Revision 1.2Feb 28, 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: Rv1155 protein
B: Rv1155 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,92419
Polymers32,4952
Non-polymers2,42917
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6820 Å2
ΔGint-8 kcal/mol
Surface area13070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.579, 65.172, 77.063
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Rv1155 protein


Mass: 16247.338 Da / Num. of mol.: 2 / Fragment: Rv1155
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: MT7199_1184 / Production host: Escherichia coli (E. coli) / References: UniProt: L0NRR9, UniProt: O06553*PLUS

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Non-polymers , 7 types, 76 molecules

#2: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Fragment: F420 / Source method: obtained synthetically / Formula: CH2O2
#3: Chemical
ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-F42 / COENZYME F420


Mass: 773.593 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H36N5O18P
#7: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.07 Å3/Da / Density % sol: 40.59 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 1, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→49.76 Å / Num. obs: 12476 / Observed criterion σ(F): 1 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→38.532 Å / SU ML: 0.34 / σ(F): 1.34 / Phase error: 28.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2541 635 5.09 %
Rwork0.1829 --
obs0.1867 12472 99.77 %
all-12476 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→38.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 137 59 2383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192378
X-RAY DIFFRACTIONf_angle_d1.4633230
X-RAY DIFFRACTIONf_dihedral_angle_d15.002847
X-RAY DIFFRACTIONf_chiral_restr0.04355
X-RAY DIFFRACTIONf_plane_restr0.029425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3002-2.47770.36771170.21672328X-RAY DIFFRACTION100
2.4777-2.7270.29811130.22432343X-RAY DIFFRACTION100
2.727-3.12150.30531240.19422337X-RAY DIFFRACTION100
3.1215-3.93210.22331400.17212359X-RAY DIFFRACTION100
3.9321-38.53690.22911410.16922470X-RAY DIFFRACTION99

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