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- PDB-2fg9: CRYSTAL STRUCTURE OF A PUTATIVE 5-NITROIMIDAZOLE ANTIBIOTIC RESIS... -

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Entry
Database: PDB / ID: 2fg9
TitleCRYSTAL STRUCTURE OF A PUTATIVE 5-NITROIMIDAZOLE ANTIBIOTIC RESISTANCE PROTEIN (BT_3078) FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.20 A RESOLUTION
Components5-nitroimidazole antibiotic resistance protein
KeywordsOXIDOREDUCTASE / PUTATIVE 5-NITROIMIDAZOLE ANTIBIOTIC RESISTANCE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
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
FLAVIN-ADENINE DINUCLEOTIDE / NICKEL (II) ION / : / 5-nitroimidazole antibiotic resistance protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of (np_811990.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 2.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 21, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_leaving_atom_flag / _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_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_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). ASSIGNMENT OF THE BIOLOGICAL SUBUNIT AS A HEXAMER IS SUPPORTED BY DATA FROM SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING. HOWEVER, THE INTERACTIONS FORMING THE HEXAMER PRIMARILY INVOLVE THE EXPRESSION TAG, SO IT IS POSSIBLE THAT THE OLIGIMERIZATION STATE OF THE WILD-TYPE PROTEIN IS DIMERIC.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 5-nitroimidazole antibiotic resistance protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9204
Polymers21,0141
Non-polymers9063
Water82946
1
A: 5-nitroimidazole antibiotic resistance protein
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)131,51924
Polymers126,0826
Non-polymers5,43818
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation38_555-y+1/2,-x+1/2,-z+1/21
crystal symmetry operation43_555-x+1/2,-z+1/2,-y+1/21
crystal symmetry operation48_555-z+1/2,-y+1/2,-x+1/21
Buried area26990 Å2
ΔGint-189 kcal/mol
Surface area39020 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)134.000, 134.000, 134.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11A-160-

NI

DetailsASSIGNMENT OF THE BIOLOGICAL SUBUNIT AS A HEXAMER IS SUPPORTED BY DATA FROM SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING. HOWEVER, THE INTERACTIONS FORMING THE HEXAMER PRIMARILY INVOLVE THE EXPRESSION TAG, SO IT IS POSSIBLE THAT THE OLIGIMERIZATION STATE OF THE WILD-TYPE PROTEIN IS DIMERIC.

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Components

#1: Protein 5-nitroimidazole antibiotic resistance protein


Mass: 21013.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: np_811990.1 / Production host: Escherichia coli (E. coli) / References: GenBank: 29340391, UniProt: Q8A377*PLUS
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.49 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.9
Details: 0.2M (NH4)2HPO4, 20.0% PEG-3350, No Buffer, pH 7.9, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.9798, 0.9797, 1.0163
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 28, 2005
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97981
20.97971
31.01631
ReflectionResolution: 2.2→28.57 Å / Num. obs: 10216 / % possible obs: 98.2 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 22.58
Reflection shell

Rmerge(I) obs: 0.755 / Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Mean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.289210.183.5520515185492
2.28-2.3798.23.96219631914
2.37-2.4898.85.2226911976
2.48-2.6198.57.22223001937
2.61-2.7798.510.11221841922
2.77-2.9899.214.65223761938
2.98-3.289924.62228971983
3.28-3.7699.438.23230271995
3.76-4.7299.354.75223591949
4.72-28.579960.58220072009

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.601data extraction
XDSdata reduction
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→28.57 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.943 / SU B: 14.012 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.206
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. DENSITY FOR RESIDUES 81-86 AND 158-159 IS DISORDERED AND NOT MODELED. 3. ASSIGNMENT OF NI IS BASED ON COORDINATION NUMBER AND GEOMETRY. ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. DENSITY FOR RESIDUES 81-86 AND 158-159 IS DISORDERED AND NOT MODELED. 3. ASSIGNMENT OF NI IS BASED ON COORDINATION NUMBER AND GEOMETRY. 4. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.245 516 4.8 %RANDOM
Rwork0.223 ---
all0.224 ---
obs0.22392 10216 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.821 Å2
Refinement stepCycle: LAST / Resolution: 2.2→28.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1296 0 58 46 1400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211430
X-RAY DIFFRACTIONr_bond_other_d0.0010.021227
X-RAY DIFFRACTIONr_angle_refined_deg1.7311.9751946
X-RAY DIFFRACTIONr_angle_other_deg0.79732844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2735172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2512465
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97215228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.604156
X-RAY DIFFRACTIONr_chiral_restr0.0840.2206
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021581
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02285
X-RAY DIFFRACTIONr_nbd_refined0.2070.2256
X-RAY DIFFRACTIONr_nbd_other0.1880.21181
X-RAY DIFFRACTIONr_nbtor_refined0.1940.2674
X-RAY DIFFRACTIONr_nbtor_other0.0940.2902
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.250
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1630.242
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2330.2100
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.210
X-RAY DIFFRACTIONr_mcbond_it1.3061.5874
X-RAY DIFFRACTIONr_mcbond_other0.2191.5348
X-RAY DIFFRACTIONr_mcangle_it1.69621367
X-RAY DIFFRACTIONr_scbond_it2.1443673
X-RAY DIFFRACTIONr_scangle_it3.3594.5579
LS refinement shellResolution: 2.2→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.359 40 -
Rwork0.288 735 -
obs--98.73 %
Refinement TLS params.Method: refined / Origin x: 40.3046 Å / Origin y: 15.5919 Å / Origin z: 49.4336 Å
111213212223313233
T-0.1806 Å2-0.051 Å2-0.0552 Å2--0.1715 Å20.1867 Å2---0.0559 Å2
L1.8804 °20.3735 °21.0221 °2-1.2117 °20.2688 °2--2.6313 °2
S0.0898 Å °-0.1507 Å °-0.4012 Å °-0.0842 Å °-0.0059 Å °-0.2156 Å °-0.0851 Å °0.0382 Å °-0.0839 Å °

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