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- PDB-1nid: THE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLA... -

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Basic information

Entry
Database: PDB / ID: 1nid
TitleTHE STRUCTURE OF CU-NITRITE REDUCTASE FROM ACHROMOBACTER CYCLOCLASTES AT FIVE PH VALUES, WITH NITRITE BOUND AND WITH TYPE II CU DEPLETED
ComponentsNITRITE REDUCTASE
KeywordsOXIDOREDUCTASE (NITRIC OXIDE(A))
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, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like ...Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter cycloclastes (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsAdman, E.T. / Godden, J.W. / Turley, S.
Citation
Journal: J.Biol.Chem. / Year: 1995
Title: The structure of copper-nitrite reductase from Achromobacter cycloclastes at five pH values, with NO2- bound and with type II copper depleted.
Authors: Adman, E.T. / Godden, J.W. / Turley, S.
#1: Journal: Science / Year: 1991
Title: The 2.3 Angstrom X-Ray Structure of Nitrite Reductase from Achromobacter Cycloclastes
Authors: Godden, J.W. / Turley, S. / Teller, D.C. / Adman, E.T. / Liu, M.Y. / Payne, W.J. / Legall, J.
#2: Journal: Biochemistry / Year: 1991
Title: Amino Acid Sequence of Nitrite Reductase: A Copper Protein from Achromobacter Cycloclastes
Authors: Fenderson, F.F. / Kumar, S. / Adman, E.T. / Liu, M.-Y. / Payne, W.J. / Legall, J.
#3: Journal: J.Mol.Biol. / Year: 1988
Title: Crystallization of Nitrite Reductase from Achromobacter Cycloclastes
Authors: Turley, S. / Adman, E.T. / Sieker, L.C. / Liu, M.-Y. / Payne, W.J. / Legall, J.
History
DepositionJul 3, 1995Processing site: BNL
Revision 1.0Dec 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.process_site / _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.ptnr1_symmetry / _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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2334
Polymers37,0601
Non-polymers1733
Water3,099172
1
A: NITRITE REDUCTASE
hetero molecules

A: NITRITE REDUCTASE
hetero molecules

A: NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,69912
Polymers111,1793
Non-polymers5199
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area13270 Å2
ΔGint-87 kcal/mol
Surface area33710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)97.600, 97.600, 97.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Atom site foot note1: CIS PROLINE - PRO 23 / 2: CIS PROLINE - PRO 69
Components on special symmetry positions
IDModelComponents
11A-1251-

HOH

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Components

#1: Protein NITRITE REDUCTASE


Mass: 37059.809 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PH 5.4 ("NT1") NITRITE SOAKED / Source: (natural) Achromobacter cycloclastes (bacteria) / References: UniProt: P25006, EC: 1.7.99.3
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsNOTE THAT A NUMBER OF WATERS HAVE OCCUPANCY GREATER THAN 1.0.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.13 %
Crystal growpH: 5.4 / Details: pH 5.4
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMpotassium phosphate1reservoir
233 %satammonium sulfate1reservoir

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Data collection

ReflectionHighest resolution: 2.2 Å / Num. obs: 15556 / % possible obs: 95 % / Observed criterion σ(I): 0
Reflection
*PLUS
Lowest resolution: 9999 Å / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 6.2

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→10 Å / σ(F): 0 / Details: HIS 306 HAS SOMEWHAT DISTORTED GEOMETRY.
RfactorNum. reflection% reflection
Rwork0.149 --
obs0.149 14536 92 %
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 5 172 2752
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.021
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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