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- PDB-2xwz: STRUCTURE OF THE RECOMBINANT NATIVE NITRITE REDUCTASE FROM ALCALI... -

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Basic information

Entry
Database: PDB / ID: 2xwz
TitleSTRUCTURE OF THE RECOMBINANT NATIVE NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS complexed with nitrite
ComponentsDISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
KeywordsOXIDOREDUCTASE / PROTON CHANNEL / DENITRIFICATION.
Function / homology
Function and homology information


denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / copper ion binding
Similarity search - Function
Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / COPPER (II) ION / NITRIC OXIDE / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesACHROMOBACTER XYLOSOXIDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsAntonyuk, S.V. / Leferink, N.G.H. / Han, C. / Heyes, D.J. / Rigby, S.E.J. / Hough, M.A. / Eady, R.R. / Scrutton, N.S. / Hasnain, S.S.
CitationJournal: Biochemistry / Year: 2011
Title: Proton-Coupled Electron Transfer in the Catalytic Cycle of Alcaligenes Xylosoxidans Copper-Dependent Nitrite Reductase.
Authors: Leferink, N.G.H. / Han, C. / Antonyuk, S.V. / Heyes, D.J. / Rigby, S.E.J. / Hough, M.A. / Eady, R.R. / Scrutton, N.S. / Hasnain, S.S.
History
DepositionNov 6, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 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 / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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.ptnr2_auth_asym_id / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
B: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
C: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
D: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
E: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
F: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,31279
Polymers219,4296
Non-polymers5,88373
Water28,3021571
1
A: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
D: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
E: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,78241
Polymers109,7153
Non-polymers3,06738
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19180 Å2
ΔGint-331.6 kcal/mol
Surface area34040 Å2
MethodPISA
2
B: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
C: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
F: DISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,53038
Polymers109,7153
Non-polymers2,81635
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18720 Å2
ΔGint-308.4 kcal/mol
Surface area33890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)173.930, 176.820, 181.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 36571.512 Da / Num. of mol.: 6 / Fragment: RESIDUES 26-360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ACHROMOBACTER XYLOSOXIDANS (bacteria) / Strain: IW2 IWASAKI / Plasmid: PET26 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O68601, nitrite reductase (NO-forming)

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Non-polymers , 6 types, 1644 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO2
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 44 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1571 / 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: 6.37 Å3/Da / Density % sol: 80 % / Description: NONE
Crystal growpH: 4.25
Details: 1.8 M LITHIUM SULFATE, 100MM ACETATE BUFFER PH 4.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 29, 2010 / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.34→43.97 Å / Num. obs: 232880 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10
Reflection shellResolution: 2.34→2.48 Å / Redundancy: 7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OE1

1oe1


Resolution: 2.34→43.97 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.629 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.19875 11648 5 %RANDOM
Rwork0.17392 ---
obs0.17516 221310 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.832 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--0.6 Å20 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.34→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15374 0 292 1571 17237
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02216139
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210604
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.96822013
X-RAY DIFFRACTIONr_angle_other_deg0.898326020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.94652035
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89124.43675
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.808152510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5951562
X-RAY DIFFRACTIONr_chiral_restr0.0920.22373
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117931
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023041
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_it0.7591.510075
X-RAY DIFFRACTIONr_mcbond_other0.1651.54088
X-RAY DIFFRACTIONr_mcangle_it1.442216215
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.27936064
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.594.55782
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: 2.342→2.403 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 795 -
Rwork0.307 15122 -
obs--96.7 %

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