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- PDB-6brd: Crystal structure of rifampin monooxygenase from Streptomyces ven... -

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Basic information

Entry
Database: PDB / ID: 6brd
TitleCrystal structure of rifampin monooxygenase from Streptomyces venezuelae, complexed with rifampin and FAD
ComponentsRifampin monooxygenase
KeywordsOXIDOREDUCTASE / rifampin / rifamycin / antibiotic resistance / monooxygenase / FAD / flavin adenine dinucleotide / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID / National Institute of Allergy and Infectious Disease
Function / homology
Function and homology information


rifampicin monooxygenase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / FAD binding
Similarity search - Function
Alpha-Beta Plaits - #2450 / Glutaredoxin - #120 / Aromatic-ring hydroxylase, C-terminal / : / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin ...Alpha-Beta Plaits - #2450 / Glutaredoxin - #120 / Aromatic-ring hydroxylase, C-terminal / : / 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 / RIFAMPICIN / Rifampicin monooxygenase
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.32 Å
AuthorsCox, G. / Kelso, J. / Stogios, P.J. / Savchenko, A. / Anderson, W.F. / Wright, G.D. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN2720120026C United States
CitationJournal: Cell Chem Biol / Year: 2018
Title: Rox, a Rifamycin Resistance Enzyme with an Unprecedented Mechanism of Action.
Authors: Koteva, K. / Cox, G. / Kelso, J.K. / Surette, M.D. / Zubyk, H.L. / Ejim, L. / Stogios, P. / Savchenko, A. / Sorensen, D. / Wright, G.D.
History
DepositionNov 30, 2017Deposition site: RCSB / Processing site: RCSB
SupersessionDec 13, 2017ID: 5VQC
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Feb 21, 2018Group: Database references
Category: citation / citation_author / pdbx_database_related
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3May 2, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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 / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Rifampin monooxygenase
B: Rifampin monooxygenase
C: Rifampin monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,61520
Polymers157,4113
Non-polymers5,20417
Water1,63991
1
A: Rifampin monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2217
Polymers52,4701
Non-polymers1,7506
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rifampin monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2097
Polymers52,4701
Non-polymers1,7396
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rifampin monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1856
Polymers52,4701
Non-polymers1,7155
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)202.026, 129.402, 74.342
Angle α, β, γ (deg.)90.00, 105.45, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-503-

CL

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Rifampin monooxygenase / ROX


Mass: 52470.309 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces venezuelae (strain ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745) (bacteria)
Strain: ATCC 10712 / CBS 650.69 / DSM 40230 / JCM 4526 / NBRC 13096 / PD 04745
Gene: SVEN_0481 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: F2R776

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Non-polymers , 5 types, 108 molecules

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


Mass: 785.550 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-RFP / RIFAMPICIN


Mass: 822.940 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C43H58N4O12 / Comment: antibiotic*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.98 Å3/Da / Density % sol: 58.66 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate, pH 6.5, 20% w/v PEG8000, 0.2 M magnesium acetate, soaked in rifamycin

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→33.417 Å / Num. obs: 27436 / % possible obs: 97.1 % / Redundancy: 5.8 % / Rsym value: 0.162 / Net I/σ(I): 5.55
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 1.33 / Rsym value: 0.443 / % possible all: 83.3

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Processing

Software
NameVersionClassification
PHENIX(dev_2733: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5KOW

5kow


Resolution: 3.32→33.417 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 21.63
RfactorNum. reflection% reflectionSelection details
Rfree0.2344 1333 5 %RANDOM
Rwork0.1845 ---
obs0.187 26650 97.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.32→33.417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10793 0 326 92 11211
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01111337
X-RAY DIFFRACTIONf_angle_d1.07915440
X-RAY DIFFRACTIONf_dihedral_angle_d20.3084029
X-RAY DIFFRACTIONf_chiral_restr0.0561724
X-RAY DIFFRACTIONf_plane_restr0.0072009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3201-3.43860.26171210.22672298X-RAY DIFFRACTION90
3.4386-3.57610.28811280.21982449X-RAY DIFFRACTION96
3.5761-3.73870.2681350.2052545X-RAY DIFFRACTION98
3.7387-3.93550.26391340.18592552X-RAY DIFFRACTION99
3.9355-4.18170.24111340.1722540X-RAY DIFFRACTION99
4.1817-4.50380.19321350.15442550X-RAY DIFFRACTION99
4.5038-4.95570.19241350.1632586X-RAY DIFFRACTION99
4.9557-5.66980.2531360.17622566X-RAY DIFFRACTION99
5.6698-7.13190.2461360.20882588X-RAY DIFFRACTION100
7.1319-33.41890.20961390.1782643X-RAY DIFFRACTION100
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)
12.3698-0.29910.93142.47290.73421.8929-0.0883-0.08580.09570.4660.2722-0.57890.10940.2551-0.1010.17730.0588-0.07710.2408-0.03860.236755.1068-7.900423.8196
25.78290.9611-0.19997.629-2.47425.96690.3760.50490.95860.0111-0.3611-1.2195-0.96921.24340.00640.5148-0.13960.16210.66090.10510.705660.67958.13181.5371
30.8541-0.12680.59161.93840.03511.4924-0.1081-0.29650.16840.5247-0.00620.1503-0.0521-0.32140.08370.2060.03290.07470.3136-0.00690.225639.3785-2.66328.5914
42.4118-0.0815-0.47711.0123-0.44733.3687-0.09070.2460.1126-0.06790.04130.14030.0850.01980.04750.1895-0.0732-0.22270.20840.02950.283314.45224.6926-15.4046
51.5585-1.12220.67231.0278-1.19282.5387-0.03030.1368-0.349-0.2905-0.03370.21470.51630.01040.10070.3442-0.0336-0.11650.2137-0.0510.32722.065511.4159-8.3128
62.45010.1828-1.32932.85460.51971.7776-0.1479-0.57920.73410.350.1150.0378-0.34670.3790.03270.52820.0463-0.33360.2725-0.09280.525516.13141.91583.9694
72.9656-0.8583-0.52442.93241.36272.41780.11140.082-0.0312-0.2161-0.06720.1924-0.2387-0.1526-0.02840.12780.00150.04930.1742-0.01910.320159.925828.226745.4765
87.70482.2477-1.45075.33721.10731.4890.23231.41710.5416-0.7812-0.05410.0453-0.8271-0.2771-0.27140.86110.07420.18270.7660.21450.602270.085638.933121.2593
92.571-1.0167-0.56151.51070.86331.88740.0252-0.3386-0.48990.1888-0.0624-0.04260.16640.18770.0250.15550.01550.00250.21910.0820.450572.243517.689650.7521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:171)
2X-RAY DIFFRACTION2(chain A and resid 172:260)
3X-RAY DIFFRACTION3(chain A and resid 261:474)
4X-RAY DIFFRACTION4(chain B and resid 1:171)
5X-RAY DIFFRACTION5(chain B and resid 172:372)
6X-RAY DIFFRACTION6(chain B and resid 373:474)
7X-RAY DIFFRACTION7(chain C and resid 1:175)
8X-RAY DIFFRACTION8(chain C and resid 176:256)
9X-RAY DIFFRACTION9(chain C and resid 257:474)

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