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- PDB-1ndr: CRYSTALLOGRAPHIC STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE FRO... -

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Basic information

Entry
Database: PDB / ID: 1ndr
TitleCRYSTALLOGRAPHIC STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS
ComponentsNITRITE REDUCTASE
KeywordsREDUCTASE / BLUE COPPER NITRITE REDUCTASE / COPPER PROTEIN / NITRITE REDUCTION
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 / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAchromobacter xylosoxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDodd, F.E. / Hasnain, S.S. / Abraham, Z.H.L. / Eady, R.R. / Smith, B.E.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1997
Title: Structures of a blue-copper nitrite reductase and its substrate-bound complex.
Authors: Dodd, F.E. / Hasnain, S.S. / Abraham, Z.H. / Eady, R.R. / Smith, B.E.
#1: Journal: Biochem.J. / Year: 1993
Title: Purification and Characterization of the Dissimilatory Nitrite Reductase from Alcaligenes Xylosoxidans Subsp. Xylosoxidans (N.C.I.M.B. 11015): Evidence for the Presence of Both Type 1 and Type 2 Copper Centers
Authors: Abraham, Z.H. / Lowe, D.J. / Smith, B.E.
History
DepositionJan 23, 1997Processing site: BNL
Revision 1.0Jul 7, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.process_site / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NITRITE REDUCTASE
B: NITRITE REDUCTASE
C: NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,7069
Polymers103,3253
Non-polymers3816
Water543
1
A: NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5693
Polymers34,4421
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5693
Polymers34,4421
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5693
Polymers34,4421
Non-polymers1272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.150, 101.720, 150.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.85139, -0.32225, -0.413872), (0.218338, -0.4997, 0.838229), (-0.476931, -0.804024, -0.35508)27.01013, 36.2076, 78.01798
2given(0.855013, 0.211982, -0.473304), (-0.323229, -0.495876, -0.805997), (-0.405557, 0.842123, -0.355461)6.36777, 89.45462, 8.22149

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Components

#1: Protein NITRITE REDUCTASE / NIR


Mass: 34441.711 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: BACTERIAL / Source: (natural) Achromobacter xylosoxidans (bacteria) / Strain: NCIMB 11015 / References: UniProt: P81445, EC: 1.7.99.3
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 % / Description: MODEL USED WITHOUT WATERS
Crystal growTemperature: 277 K / pH: 4.6
Details: 28% PEG 4000, 0.1M SODIUM ACETATE, PH 4.6, 4 DEGREES C, temperature 277K
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
128 %PEG40001reservoir
20.1 Msodium acetate1reservoir
30.2 Mammonium acetate1reservoir
428 %PEG40001drop
50.1 Msodium acetate1drop
60.2 Mammonium acetate1drop
710 mg/mlAxNiR1drop
820 mMMES1drop

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Data collection

DiffractionMean temperature: 286 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.92
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 16, 1995 / Details: BENT FUSED QUARTZ MIRROR
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 3→60.5 Å / Num. obs: 16691 / % possible obs: 79.3 % / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 8.1
Reflection shellResolution: 3→3.08 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 4.1 / % possible all: 57.4
Reflection
*PLUS
Num. measured all: 53045
Reflection shell
*PLUS
% possible obs: 57.6 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
WEISdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NITRITE REDUCTASE PDB CODE 1AFN

1afn
PDB Unreleased entry


Resolution: 3→8 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: R-FREE / σ(F): 2
Details: THIS IS AN ALPHA CARBON ENTRY. THE SIDE CHAINS FOR HIS 95 HIS 100, HIS 135, CYS 136, HIS 145, HIS 306 AND ONE SOLVENT MOLECULE, HOH 503 WHICH ARE INVOLVED IN COPPER COORDINATION ARE ALSO ...Details: THIS IS AN ALPHA CARBON ENTRY. THE SIDE CHAINS FOR HIS 95 HIS 100, HIS 135, CYS 136, HIS 145, HIS 306 AND ONE SOLVENT MOLECULE, HOH 503 WHICH ARE INVOLVED IN COPPER COORDINATION ARE ALSO INCLUDED. SIDE CHAINS FOR MET 150 ARE ALSO INCLUDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.27 1066 6.5 %RANDOM
Rwork0.203 ---
obs0.203 16691 75.8 %-
Displacement parametersBiso mean: 15.6 Å2
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7278 0 6 3 7287
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
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_deg2.9
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.7
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
LS refinement shellResolution: 3→3.13 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.374 --
Rwork0.276 1192 -
obs--51.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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