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- PDB-6c7s: Structure of Rifampicin Monooxygenase with Product Bound -

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Basic information

Entry
Database: PDB / ID: 6c7s
TitleStructure of Rifampicin Monooxygenase with Product Bound
ComponentsPutative rifampin monooxygenase
KeywordsOXIDOREDUCTASE / Rifampicin
Function / homology
Function and homology information


rifampicin monooxygenase / : / ubiquinone biosynthetic process / FAD binding
Similarity search - Function
Alpha-Beta Plaits - #2450 / Aromatic-ring hydroxylase, C-terminal / Glutaredoxin - #120 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / FAD/NAD(P)-binding domain superfamily ...Alpha-Beta Plaits - #2450 / Aromatic-ring hydroxylase, C-terminal / Glutaredoxin - #120 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-RFH / Rifampicin monooxygenase
Similarity search - Component
Biological speciesNocardia farcinica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLiu, L.-K. / Tanner, J.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1506206 United States
National Science Foundation (NSF, United States)MCB 1021384 United States
CitationJournal: Biochemistry / Year: 2018
Title: Structural Evidence for Rifampicin Monooxygenase Inactivating Rifampicin by Cleaving Its Ansa-Bridge.
Authors: Liu, L.K. / Dai, Y. / Abdelwahab, H. / Sobrado, P. / Tanner, J.J.
History
DepositionJan 23, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_audit_support / pdbx_entity_nonpoly
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_audit_support.funding_organization / _pdbx_entity_nonpoly.name
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative rifampin monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6927
Polymers51,7181
Non-polymers1,9756
Water5,837324
1
A: Putative rifampin monooxygenase
hetero molecules

A: Putative rifampin monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,38514
Polymers103,4352
Non-polymers3,94912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/61
Buried area6230 Å2
ΔGint-97 kcal/mol
Surface area36320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.877, 81.877, 286.205
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-802-

HOH

21A-917-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative rifampin monooxygenase


Mass: 51717.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nocardia farcinica (strain IFM 10152) (bacteria)
Strain: IFM 10152 / Gene: rox, NFA_35380 / Cell line (production host): TurboCells from Genlantis / Production host: Escherichia coli (E. coli) / References: UniProt: Q5YTV5

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Non-polymers , 5 types, 330 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-RFH / (1E,3S,4R,5S,6R,7R,8R,9S,10S,11E,13E)-15-amino-1-{[(2S)-5,7-dihydroxy-2,4-dimethyl-8-{(E)-[(4-methylpiperazin-1-yl)imino]methyl}-1,6,9-trioxo-1,2,6,9-tetrahydronaphtho[2,1-b]furan-2-yl]oxy}-7,9-dihydroxy-3-methoxy-4,6,8,10,14-pentamethyl-15-oxopentadeca-1,11,13-trien-5-yl acetate


Mass: 838.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H58N4O13 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.68 Å3/Da / Density % sol: 54.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: The reservoir contained 24% (w/v) PEG 3350, 200 mM magnesium chloride. The protein stock solution included 5 mM RIF, 100 mM NADPH and 100 mM dithionite.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→63.54 Å / Num. obs: 33890 / % possible obs: 98.6 % / Redundancy: 18.8 % / Biso Wilson estimate: 26.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.021 / Rrim(I) all: 0.094 / Net I/σ(I): 25.3 / Num. measured all: 636732 / Scaling rejects: 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.1613.30.69123450.8430.1920.7286.6
8.91-63.5416.20.0315790.9990.0080.03299.3

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Processing

Software
NameVersionClassification
Aimless0.5.32data scaling
PHENIX1.10_2155refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KOW

5kow


Resolution: 2.1→63.536 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0.19 / Phase error: 24.14
RfactorNum. reflection% reflection
Rfree0.2411 3021 4.98 %
Rwork0.1999 --
obs0.202 60602 96.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.02 Å2 / Biso mean: 30.7286 Å2 / Biso min: 15.06 Å2
Refinement stepCycle: final / Resolution: 2.1→63.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3614 0 125 324 4063
Biso mean--38.86 33.67 -
Num. residues----473
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023840
X-RAY DIFFRACTIONf_angle_d0.6845241
X-RAY DIFFRACTIONf_chiral_restr0.044582
X-RAY DIFFRACTIONf_plane_restr0.004684
X-RAY DIFFRACTIONf_dihedral_angle_d18.3122244
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 22

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.13280.31941300.25052246237686
2.1328-2.16780.30711040.25812398250287
2.1678-2.20520.30481500.27922577272795
2.2052-2.24530.54231220.48922185230782
2.2453-2.28850.62621260.46472218234481
2.2885-2.33520.28781180.234927282846100
2.3352-2.3860.23761330.212926792812100
2.386-2.44150.25781470.205227112858100
2.4415-2.50250.24791580.203426792837100
2.5025-2.57020.25131300.202627392869100
2.5702-2.64580.26631360.208727062842100
2.6458-2.73120.27811390.207127302869100
2.7312-2.82890.25361120.210727252837100
2.8289-2.94210.28051560.219626782834100
2.9421-3.0760.28821490.208227002849100
3.076-3.23820.19851410.205727052846100
3.2382-3.44110.21691560.183726912847100
3.4411-3.70670.18161380.193427122850100
3.7067-4.07970.19471350.16152686282199
4.0797-4.66990.16911220.13527022824100
4.6699-5.88290.17281510.152427152866100
5.8829-63.56460.2191680.159226712839100

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