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- PDB-2x1k: H71S mutant of the antibiotic resistance protein NimA from Deinoc... -

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Basic information

Entry
Database: PDB / ID: 2x1k
TitleH71S mutant of the antibiotic resistance protein NimA from Deinococcus radiodurans
ComponentsNIMA-RELATED PROTEIN
KeywordsOXIDOREDUCTASE / ANTIBIOTIC RESISTANCE
Function / homologyPyridoxamine 5'-phosphate oxidase-related / Pyridoxamine 5'-phosphate oxidase / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / FMN-binding split barrel / Roll / Mainly Beta / ACETATE ION / NimA-related protein
Function and homology information
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLeiros, H.S. / Brandsdal, B.O. / McSweeney, S.M.
Citation
Journal: Biochim.Biophys.Acta / Year: 2010
Title: Biophysical Characterization and Mutational Analysis of the Antibiotic Resistance Protein Nima from Deinococcus Radiodurans.
Authors: Leiros, H.S. / Brandsdal, B.O. / Mcsweeney, S.M.
#1: Journal: J.Biol.Chem. / Year: 2004
Title: Structural Basis of 5-Nitroimidazole Antibiotic Resistance: The Crystal Structure of Nima from Deinococcus Radiodurans.
Authors: Leiros, H.-K.S. / Kozielski-Stuhrmann, S. / Kapp, U. / Terradot, L. / Leonard, G.A. / Mcsweeney, S.M.
History
DepositionJan 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NIMA-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5163
Polymers24,3981
Non-polymers1182
Water5,026279
1
A: NIMA-RELATED PROTEIN
hetero molecules

A: NIMA-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0326
Polymers48,7962
Non-polymers2364
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5510 Å2
ΔGint-47.9 kcal/mol
Surface area24620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.899, 38.969, 59.792
Angle α, β, γ (deg.)90.00, 113.89, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NIMA-RELATED PROTEIN / 5-NITROIMIDAZOLE REDUCTASE / NIMA REDUCTASE


Mass: 24398.127 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 STAR(DE3)PLYSS / References: UniProt: Q9RW27
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 71 TO SER

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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: 2.33 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 6
Details: 13MG/ML PROTEIN, 0.6M SODIUM ACETATE, 0.1M BUFFER PH 6 (CITRATE/MES).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.55→20 Å / Num. obs: 29814 / % possible obs: 96.7 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 0
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 0 / % possible all: 79.8

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W3O

1w3o


Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.615 / SU ML: 0.06 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23427 1494 5 %RANDOM
Rwork0.18128 ---
obs0.1839 28320 96.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.861 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20.78 Å2
2--0.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.55→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1651 0 8 279 1938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211729
X-RAY DIFFRACTIONr_bond_other_d0.0010.021176
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9452361
X-RAY DIFFRACTIONr_angle_other_deg1.40532833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0475214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.69922.98987
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.31615264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5331517
X-RAY DIFFRACTIONr_chiral_restr0.1130.2248
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211988
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02375
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0621.51063
X-RAY DIFFRACTIONr_mcbond_other0.3161.5422
X-RAY DIFFRACTIONr_mcangle_it1.81621710
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5463666
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.8494.5651
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 98 -
Rwork0.271 1564 -
obs--73.74 %

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