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- PDB-2hw2: Crystal structure of Rifampin ADP-ribosyl transferase in complex ... -

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Basic information

Entry
Database: PDB / ID: 2hw2
TitleCrystal structure of Rifampin ADP-ribosyl transferase in complex with Rifampin
ComponentsRifampin ADP-ribosyl transferase
KeywordsTRANSFERASE / PROTEIN-ANTIBIOTIC COMPLEX / ADP-RIBOSYLATION / RIFAMPIN
Function / homology
Function and homology information


transferase activity
Similarity search - Function
Rifampin ADP-ribosyltransferase domain / Rifampin ADP-ribosyltransferase / Rifampin ADP-ribosyltransferase superfamily / Rifampin ADP-ribosyl transferase / ADP-ribosylation fold / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
GLYCINE / RIFAMPICIN / Rifampin ADP-ribosyl transferase / Rifampin ADP-ribosyl transferase
Similarity search - Component
Biological speciesMycobacterium smegmatis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsBaysarowich, J. / Wright, G.D. / Junop, M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: Rifamycin antibiotic resistance by ADP-ribosylation: Structure and diversity of Arr.
Authors: Baysarowich, J. / Koteva, K. / Hughes, D.W. / Ejim, L. / Griffiths, E. / Zhang, K. / Junop, M. / Wright, G.D.
History
DepositionJul 31, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 11, 2012Group: Other
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE The difference in sequence is due to a different strain of Mycobacterium smegmatis mc2-155 ...SEQUENCE The difference in sequence is due to a different strain of Mycobacterium smegmatis mc2-155 used for crystallization (Alexander, D., Jones, J., and Liu, J. (2003) Antimicrobial Agents and Chemotherapy, 47, 3208-3213)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rifampin ADP-ribosyl transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8494
Polymers15,8761
Non-polymers9733
Water4,576254
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.663, 61.041, 45.567
Angle α, β, γ (deg.)90.00, 91.81, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1275-

HOH

DetailsThe biological unit is a monomer.

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Components

#1: Protein Rifampin ADP-ribosyl transferase


Mass: 15875.920 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium smegmatis (bacteria) / Gene: arr / Plasmid: pET22b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O67972, UniProt: A0QRS5*PLUS, NAD+ ADP-ribosyltransferase
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-RFP / RIFAMPICIN


Mass: 822.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C43H58N4O12 / Comment: antibiotic*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 2.42 Å3/Da / Density % sol: 49.07 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 30% MPD, 5% PEG 8000, 0.005M magesium chloride, 0.001M rifampin, 0.03M glycylglycine, 0.05M tris, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 11, 2006
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.45→30.18 Å / Num. all: 26649 / Num. obs: 26649 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.6
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 4 % / Rmerge(I) obs: 0.544 / Mean I/σ(I) obs: 2.7 / Num. unique all: 2578 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→30.18 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.501 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.068 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.18546 1342 5 %RANDOM
Rwork0.13421 ---
obs0.13698 25293 97.95 %-
all-25293 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.554 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å2-0.85 Å2
2---0.44 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.45→30.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1080 0 68 254 1402
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0221215
X-RAY DIFFRACTIONr_angle_refined_deg2.1862.0241663
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6835148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26623.21456
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.20715191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6931512
X-RAY DIFFRACTIONr_chiral_restr0.1360.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02962
X-RAY DIFFRACTIONr_nbd_refined0.240.2597
X-RAY DIFFRACTIONr_nbtor_refined0.320.2837
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2196
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3230.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1950.215
X-RAY DIFFRACTIONr_mcbond_it2.4781.5727
X-RAY DIFFRACTIONr_mcangle_it3.32521145
X-RAY DIFFRACTIONr_scbond_it4.4923610
X-RAY DIFFRACTIONr_scangle_it6.1964.5514
LS refinement shellResolution: 1.45→1.486 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 85 -
Rwork0.143 1847 -
obs--95.5 %
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)
10.92020.6414-0.00371.5162-0.34911.0968-0.08580.0232-0.0014-0.05510.0176-0.1142-0.05680.1070.0682-0.06320.0022-0.0074-0.054-0.0012-0.0613-16.4841.868-10.31
221.07756.798-7.701314.06772.73125.1041-0.4366-0.7064-0.2625-0.47340.3650.2567-0.01670.4670.07160.06520.0137-0.01610.059-0.00480.0626-19.9082.959-13.854
30.50930.4492-0.27860.5817-0.18270.7514-0.04630.0001-0.0202-0.04570.0275-0.0369-0.01510.05860.01880.05320.0059-0.0050.0631-0.01160.0532-17.042.437-10.959
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 143
2X-RAY DIFFRACTION1A1200
3X-RAY DIFFRACTION2A144 - 145
4X-RAY DIFFRACTION3A1201 - 1454

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