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- PDB-1hau: X-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND... -

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Basic information

Entry
Database: PDB / ID: 1hau
TitleX-RAY STRUCTURE OF A BLUE COPPER NITRITE REDUCTASE AT HIGH PH AND IN COPPER FREE FORM AT 1.9 A RESOLUTION
ComponentsDISSIMILATORY COPPER-CONTAINING NITRITE REDUCTASE
KeywordsOXIDOREDUCTASE / NITRITE REDUCTASE / COPPER / BLUE COPPER / OXIDOREDUCTASE OXIDOREDUCTASE
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
COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesALCALIGENES XYLOSOXYDANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEllis, M.J. / Dodd, F.E. / Strange, R.W. / Prudencio, M. / Sawerseady, R.R. / Hasnain, S.S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: X-Ray Structure of a Blue Copper Nitrite Reductase at High Ph and in Copper-Free Form at 1.9 A Resolution
Authors: Ellis, M.J. / Dodd, F.E. / Strange, R.W. / Prudencio, M. / Sawers, G. / Eady, R.R. / Hasnain, S.S.
History
DepositionApr 9, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 2, 2001Provider: repository / Type: Initial release
Revision 1.1May 9, 2012Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,6983
Polymers36,5711
Non-polymers1272
Water3,189177
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)110,0939
Polymers109,7123
Non-polymers3816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area13540 Å2
ΔGint-91.9 kcal/mol
Surface area35090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.978, 80.978, 99.781
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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


Mass: 36570.527 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ALCALIGENES XYLOSOXYDANS (bacteria) / Cellular location: PERIPLASM / Strain: XYLOSOXIDANS
References: UniProt: O68601, EC: 1.7.99.3, nitrite reductase (NO-forming)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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: 2.62 Å3/Da / Density % sol: 52.75 %
Description: DATA WERE COLLECTED USING THE WEISSENBERG METHOD
Crystal growpH: 8.5
Details: 30% PEG 4K, 0.1M MAGNESIUM CHLORIDE, 0.1M TRIS-HCL PH8.5, pH 8.50
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
125-30 %PEG40001drop
20.1 M1dropMgCl2
30.1 MTris-HCl1drop
45 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Jun 1, 1999 / Details: TORROIDAL MIRROR
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→33.15 Å / Num. obs: 26943 / % possible obs: 92.3 % / Redundancy: 3.3 % / Biso Wilson estimate: 11.19 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.4 / % possible all: 83.9
Reflection
*PLUS
Num. measured all: 87968
Reflection shell
*PLUS
% possible obs: 83.9 % / Num. unique obs: 3559 / Num. measured obs: 10194 / Rmerge(I) obs: 0.31

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
CCP4data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NDT MONOMER

1ndt


Resolution: 1.9→20 Å / SU B: 2.06 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.124 / ESU R Free: 0.123
Details: RESIDUES WITH ZERO OCCUPANCY, NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1406 5 %RANDOM
Rwork0.154 ---
obs0.156 25520 91.3 %-
Displacement parametersBiso mean: 18.47 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2575 0 2 177 2754
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0280.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.2052
X-RAY DIFFRACTIONp_mcangle_it1.7243
X-RAY DIFFRACTIONp_scbond_it1.672
X-RAY DIFFRACTIONp_scangle_it2.5833
X-RAY DIFFRACTIONp_plane_restr0.0280.05
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1640.3
X-RAY DIFFRACTIONp_multtor_nbd0.2350.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1150.3
X-RAY DIFFRACTIONp_planar_tor4.87
X-RAY DIFFRACTIONp_staggered_tor13.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.220
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS

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