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- PDB-1oe1: Atomic Resolution Structure of the Wildtype Native Nitrite Reduct... -

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Basic information

Entry
Database: PDB / ID: 1oe1
TitleAtomic Resolution Structure of the Wildtype Native Nitrite Reductase from Alcaligenes xylosoxidans
ComponentsDISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
KeywordsREDUCTASE / DENITRIFICATION / NITRITE REDUCTASE
Function / homology
Function and homology information


denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / ferroxidase activity / nitrate assimilation / outer membrane-bounded periplasmic space / copper ion binding
Similarity search - Function
Nitrite reductase, copper-type / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesALCALIGENES XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.04 Å
AuthorsEllis, M.J. / Dodd, F.E. / Hasnain, S.S.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Atomic Resolution Structures of Native Copper Nitrite Reductase from Alcaligenes Xylosoxidans and the Active Site Mutant Asp92Glu
Authors: Ellis, M.J. / Dodd, F.E. / Sawers, G. / Eady, R.R. / Hasnain, S.S.
History
DepositionMar 18, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 17, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 11, 2020Group: Derived calculations / Polymer sequence / Category: entity_poly / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8754
Polymers36,5531
Non-polymers3213
Water8,359464
1
A: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules

A: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules

A: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,62412
Polymers109,6603
Non-polymers9649
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.725, 78.725, 98.885
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-2057-

HOH

21A-2092-

HOH

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Components

#1: Protein DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE / NITRITE REDUCTASE / NIR


Mass: 36553.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: WILDTYPE NATIVE PROTEIN FROM ALCAILGENES XYLOSOXIDANS
Source: (natural) ALCALIGENES XYLOSOXIDANS (bacteria) / References: UniProt: O68601
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.4 Å3/Da / Density % sol: 49.2 % / Description: DATA WERE COLLECTED USING OSCILLATION METHOD
Crystal growpH: 6.5 / Details: 40-50% PEG-MME 550, 0.1M MES PH 6.5, 10MM CUSO4
Crystal grow
*PLUS
Temperature: 21 ℃ / pH: 7.1 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
135 %(w/v)PEG550 MME1reservoir
210 mM1reservoirZnSO4
30.1 MMES1reservoirpH6.5
410 mg/mlprotein1drop
510 mMTris-HCl1droppH7.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 15, 2001 / Details: MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.04→60 Å / Num. obs: 167110 / % possible obs: 96.6 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 19.1
Reflection shellResolution: 1.04→1.06 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.3 / % possible all: 93.1
Reflection
*PLUS
Lowest resolution: 60 Å / Num. measured all: 1766001
Reflection shell
*PLUS
% possible obs: 93.1 % / Num. unique obs: 7735 / Num. measured obs: 17252 / Rmerge(I) obs: 0.333

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Processing

Software
NameClassification
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HAU

1hau


Resolution: 1.04→60 Å / Num. parameters: 27952 / Num. restraintsaints: 33870 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: NO GEOMETRIC OR ADP RESTRAINTS APPLIED TO COPPER ATOMS. DISORDERED SIDE CHAINS INCLUDED DUE TO KNOWN SEQUENCE
RfactorNum. reflection% reflectionSelection details
Rfree0.1416 3245 2 %RANDOM
all0.1175 162462 --
obs0.1193 -97.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER
Refine analyzeNum. disordered residues: 18 / Occupancy sum non hydrogen: 3106
Refinement stepCycle: LAST / Resolution: 1.04→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 15 464 3027
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0352
X-RAY DIFFRACTIONs_zero_chiral_vol0.093
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.035
X-RAY DIFFRACTIONs_approx_iso_adps0.087
Software
*PLUS
Name: SHELX / Version: 97 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.13 / Rfactor Rwork: 0.117
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_plane_restr0.0352
X-RAY DIFFRACTIONx_chiral_restr0.093

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