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- PDB-2vpa: High resolution crystal structure of the antibiotic resistance pr... -

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Basic information

Entry
Database: PDB / ID: 2vpa
TitleHigh resolution crystal structure of the antibiotic resistance protein NimA from Deinococcus radiodurans
ComponentsNIMA-RELATED PROTEIN
KeywordsOXIDOREDUCTASE / COFACTOR / ATOMIC RESOLUTION
Function / homology
Function and homology information


Pyridoxamine 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
Similarity search - Domain/homology
ACETATE ION / PYRUVIC ACID / NimA-related protein
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsLeiros, H.-K.S. / Tedesco, C. / McSweeney, S.M.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2008
Title: High-Resolution Structure of the Antibiotic Resistance Protein Nima from Deinococcus Radiodurans.
Authors: Leiros, H.-K.S. / Tedesco, C. / 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
DepositionFeb 27, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_validate_close_contact / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_validate_close_contact.auth_atom_id_1 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)24,6143
Polymers24,4671
Non-polymers1472
Water7,314406
1
A: NIMA-RELATED PROTEIN
hetero molecules

A: NIMA-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2296
Polymers48,9342
Non-polymers2944
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5770 Å2
ΔGint-34.3 kcal/mol
Surface area23650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.037, 38.951, 59.897
Angle α, β, γ (deg.)90.00, 114.36, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 24467.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: INCLUDES THE FIRST 10 RESIDUES OF THE 21 RESIDUE LONG N-TERMINAL HIS TAG
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RW27
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE VECTOR PDEST17 (INVITROGEN) WITH A 21 RESIDUE LONG HIS- TAG (MSYYHHHHHHLESTSLYKKAG) IS ATTACHED ...THE VECTOR PDEST17 (INVITROGEN) WITH A 21 RESIDUE LONG HIS- TAG (MSYYHHHHHHLESTSLYKKAG) IS ATTACHED TO THE PROTEIN

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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: 1.75 Å3/Da / Density % sol: 43.35 % / Description: NONE
Crystal growDetails: 0.6-0.7 M SODIUM ACETATE AND 0.1 M MES PH 6 OR 0.1 M NA CACODYLATE PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9999
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 1.2→20 Å / Num. obs: 65888 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 8.16 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 10.2
Reflection shellResolution: 1.2→1.26 Å / Redundancy: 5 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.3.0021refinement
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W3O

1w3o


Resolution: 1.2→20 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.228 / SU ML: 0.025 / Cross valid method: THROUGHOUT / ESU R: 0.038 / ESU R Free: 0.04 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18 2004 3 %RANDOM
Rwork0.141 ---
obs0.142 63865 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.82 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20.2 Å2
2---0.05 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 10 406 2053
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211806
X-RAY DIFFRACTIONr_bond_other_d0.0020.021231
X-RAY DIFFRACTIONr_angle_refined_deg1.7341.9392475
X-RAY DIFFRACTIONr_angle_other_deg1.01232961
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7755227
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.34222.73795
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75615275
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9771520
X-RAY DIFFRACTIONr_chiral_restr0.1160.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022116
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02406
X-RAY DIFFRACTIONr_nbd_refined0.2450.2335
X-RAY DIFFRACTIONr_nbd_other0.2230.21331
X-RAY DIFFRACTIONr_nbtor_refined0.1830.2870
X-RAY DIFFRACTIONr_nbtor_other0.0910.2997
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2580.2292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1130.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2520.2114
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.262
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1251.51389
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.60721777
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4763830
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3594.5698
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: 1.2→1.23 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.337 158
Rwork0.255 4633

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