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- PDB-5vqb: Crystal structure of rifampin monooxygenase from Streptomyces ven... -

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Basic information

Entry
Database: PDB / ID: 5vqb
TitleCrystal structure of rifampin monooxygenase from Streptomyces venezuelae, complex with 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 / FAD/NAD(P)-binding domain superfamily ...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 / FAD/NAD(P)-binding domain superfamily / Glutaredoxin / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Rifampicin monooxygenase
Similarity search - Component
Biological speciesStreptomyces venezuelae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.391 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)HHSN27220120026C 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
DepositionMay 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: 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 / _pdbx_database_related.db_id
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 / 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

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)160,14315
Polymers157,4113
Non-polymers2,73212
Water1,08160
1
A: Rifampin monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3625
Polymers52,4701
Non-polymers8924
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Rifampin monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4907
Polymers52,4701
Non-polymers1,0196
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Rifampin monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2913
Polymers52,4701
Non-polymers8212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)203.085, 129.285, 75.311
Angle α, β, γ (deg.)90.00, 105.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Rifampin monooxygenase


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 (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: F2R776
#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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 3.03 Å3/Da / Density % sol: 59.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6, 0.2 M ammonium sulfate, 25% PEG 5K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 10, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.391→48.92 Å / Num. obs: 25915 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rpim(I) all: 0.173 / Rsym value: 0.288 / Net I/σ(I): 5.7
Reflection shellResolution: 3.4→3.46 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.68 / Num. unique obs: 1305 / CC1/2: 0.457 / Rpim(I) all: 0.565 / Rsym value: 0.928 / % possible all: 100

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Processing

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

5kow


Resolution: 3.391→48.92 Å / SU ML: 0.45 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2836 1295 5 %RANDOM
Rwork0.2255 ---
obs0.2284 25896 99.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.391→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10623 0 173 60 10856
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00111006
X-RAY DIFFRACTIONf_angle_d0.44714968
X-RAY DIFFRACTIONf_dihedral_angle_d17.8013931
X-RAY DIFFRACTIONf_chiral_restr0.041682
X-RAY DIFFRACTIONf_plane_restr0.0031953
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3906-3.52630.35281370.30842595X-RAY DIFFRACTION95
3.5263-3.68680.34721440.27932726X-RAY DIFFRACTION100
3.6868-3.88110.34281440.25292758X-RAY DIFFRACTION100
3.8811-4.12410.30371450.23082735X-RAY DIFFRACTION100
4.1241-4.44230.24381450.19872770X-RAY DIFFRACTION100
4.4423-4.8890.23681440.19012725X-RAY DIFFRACTION100
4.889-5.59560.23111450.20292751X-RAY DIFFRACTION100
5.5956-7.04650.31071450.23542776X-RAY DIFFRACTION100
7.0465-48.92480.25461460.20062765X-RAY DIFFRACTION99
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)
18.5354-1.8352-1.11455.25993.04565.8790.1165-0.0608-0.41260.50390.4698-0.38450.07870.1813-0.36730.3040.0883-0.17730.2573-0.04270.20359.2717-12.686626.9855
22.0067-0.66120.44753.25920.95672.1329-0.13770.0320.04260.16320.3145-0.19490.0270.1096-0.16550.22020.0466-0.04940.21340.04910.190954.6482-6.026723.6254
37.8563-1.1234-0.00950.3488-1.10256.4456-0.37421.20651.6497-0.558-0.4753-0.63020.13940.97860.74511.0983-0.22190.21211.21860.43781.133860.33047.96641.1435
43.47120.8477-0.43794.18921.20935.29380.02570.20510.1543-0.27920.09960.44050.1344-0.3063-0.02490.15090.08550.04410.33170.05310.095746.8639-10.880520.3791
51.1137-0.3558-0.15625.2145-2.38034.1952-0.2051-0.2958-0.05640.20410.1417-0.0146-0.1816-0.3890.12220.13230.0901-0.00720.34790.07980.257938.23331.731516.5731
64.74241.5785-1.47592.578-1.36932.64550.1584-0.5070.69340.7863-0.3070.4377-0.2128-0.50370.06280.54480.01580.12070.4549-0.10990.243337.5131-1.055742.6175
72.2833-0.0059-0.09931.4862-0.66423.1556-0.08110.3474-0.05890.0784-0.03670.003-0.0865-0.03040.11280.4181-0.1228-0.25490.23090.07140.308914.146825.2029-15.6154
80.0611-0.05250.13120.1827-0.06610.2977-0.1516-0.23570.14160.365-0.41590.2574-0.0794-0.49990.29281.4119-0.06420.33310.8-0.56031.966522.61570.7621-13.7177
93.68155.3565-3.88728.9872-4.58185.070.69210.3146-0.0994-0.8333-2.218-4.41430.34452.52961.58282.06940.40630.60112.0461.46264.124414.5588-6.9537-0.1342
109.12420.55635.35846.49963.25554.47480.3308-0.4965-4.04280.74790.2490.39421.5587-0.3328-0.44021.72770.01930.28130.9454-0.06922.134718.3785-1.9107-12.3963
110.88840.2096-0.67932.4514-0.67451.9016-0.2705-0.17910.3157-0.03210.0153-0.4228-0.17570.2763-0.28080.4797-0.108-0.38490.21560.02410.243724.661629.7867-12.7727
122.0802-0.4745-0.02851.6632-0.63920.5361-0.1496-0.28240.49430.14580.0188-0.0098-0.30270.0190.10910.61130.0283-0.27030.3037-0.05850.375819.830732.46724.0031
131.46-0.5399-0.29023.28231.75194.31710.1474-0.20330.0909-0.2126-0.09650.0946-0.13150.0863-0.02530.1766-0.0441-0.01670.2666-0.0360.559159.67928.126446.0157
149.13021.79251.08346.4318-0.90324.5115-1.62952.2143-1.0894-2.14820.1841-2.0204-1.66642.32941.44672.5174-0.55060.60151.67770.20911.737970.884735.577720.969
155.55612.18076.20255.55234.80738.308-1.20870.1572-1.2334-1.7930.4734-2.1334-1.48170.87590.73231.9649-0.00780.56611.14930.71542.14467.500945.751425.2994
163.0777-0.00621.18335.4645-1.13494.5679-0.1567-0.10960.22610.2023-0.1439-0.8754-0.11170.2170.2630.28420.0156-0.05660.2556-0.06750.680168.95428.814852.8453
175.6405-0.4603-2.40353.5447-0.87768.88810.2681-0.0092-0.027-0.2887-0.0041-0.3698-0.05260.6186-0.25170.14910.0368-0.0650.4379-0.08410.631584.771323.974838.0539
184.21460.8896-1.77351.78931.90744.4833-0.2387-0.7555-0.57870.73080.1406-0.32570.77680.21860.07620.65120.1689-0.14210.47960.08570.634668.33874.703855.9912
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:41)
2X-RAY DIFFRACTION2(chain A and resid 42:167)
3X-RAY DIFFRACTION3(chain A and resid 168:257)
4X-RAY DIFFRACTION4(chain A and resid 258:308)
5X-RAY DIFFRACTION5(chain A and resid 309:385)
6X-RAY DIFFRACTION6(chain A and resid 386:474)
7X-RAY DIFFRACTION7(chain B and resid 1:168)
8X-RAY DIFFRACTION8(chain B and resid 169:184)
9X-RAY DIFFRACTION9(chain B and resid 185:197)
10X-RAY DIFFRACTION10(chain B and resid 198:260)
11X-RAY DIFFRACTION11(chain B and resid 261:332)
12X-RAY DIFFRACTION12(chain B and resid 333:474)
13X-RAY DIFFRACTION13(chain C and resid 1:171)
14X-RAY DIFFRACTION14(chain C and resid 172:220)
15X-RAY DIFFRACTION15(chain C and resid 221:256)
16X-RAY DIFFRACTION16(chain C and resid 257:334)
17X-RAY DIFFRACTION17(chain C and resid 335:385)
18X-RAY DIFFRACTION18(chain C and resid 386:474)

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