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- PDB-1bq5: NITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS GIFU 1051 -

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Basic information

Entry
Database: PDB / ID: 1bq5
TitleNITRITE REDUCTASE FROM ALCALIGENES XYLOSOXIDANS GIFU 1051
ComponentsNITRITE REDUCTASE
KeywordsOXIDOREDUCTASE / NITRITE REDUCTASE / CUPROPROTEIN
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 / 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 speciesAchromobacter xylosoxidans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsInoue, T. / Gotowda, M. / Deligeer / Suzuki, S. / Kataoka, K. / Yamaguchi, K. / Watanabe, H. / Goho, M. / Yasushi, K.A.I.
CitationJournal: J.Biochem.(Tokyo) / Year: 1998
Title: Type 1 Cu structure of blue nitrite reductase from Alcaligenes xylosoxidans GIFU 1051 at 2.05 A resolution: comparison of blue and green nitrite reductases.
Authors: Inoue, T. / Gotowda, M. / Deligeer / Kataoka, K. / Yamaguchi, K. / Suzuki, S. / Watanabe, H. / Gohow, M. / Kai, Y.
History
DepositionAug 21, 1998Processing site: BNL
Revision 1.0Aug 21, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_ref_seq_dif.details / _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: NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2563
Polymers37,1291
Non-polymers1272
Water2,000111
1
A: NITRITE REDUCTASE
hetero molecules

A: NITRITE REDUCTASE
hetero molecules

A: NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7699
Polymers111,3873
Non-polymers3816
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area13490 Å2
ΔGint-85 kcal/mol
Surface area33340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)106.565, 106.565, 63.578
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 NITRITE REDUCTASE


Mass: 37129.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Achromobacter xylosoxidans (bacteria) / Strain: GIFU 1051 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.77 Å3/Da / Density % sol: 55 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
20.1 MTris-HCl1drop
30.2 Msodium acetate1drop
412 %PEG40001drop
524 %PEG40001reservoir
60.1 MTris-HCl1reservoir
70.2 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Jun 3, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→91.78 Å / Num. obs: 23309 / % possible obs: 87.3 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 31.1 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.9
Reflection shellResolution: 2.05→2.25 Å / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 3.8 / % possible all: 78.7
Reflection
*PLUS
Num. measured all: 89691
Reflection shell
*PLUS
% possible obs: 78.7 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NIR FROM ACHROMOBACTER CYCLOCLASTES

Resolution: 2.05→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1065 5 %RANDOM
Rwork0.18 ---
obs-20280 77.1 %-
Displacement parametersBiso mean: 23.9 Å2
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 2 111 2657
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0280.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1862
X-RAY DIFFRACTIONp_mcangle_it1.9043
X-RAY DIFFRACTIONp_scbond_it1.4762
X-RAY DIFFRACTIONp_scangle_it2.3213
X-RAY DIFFRACTIONp_plane_restr0.0230.03
X-RAY DIFFRACTIONp_chiral_restr0.140.15
X-RAY DIFFRACTIONp_singtor_nbd0.1840.3
X-RAY DIFFRACTIONp_multtor_nbd0.2380.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1380.3
X-RAY DIFFRACTIONp_planar_tor5.17
X-RAY DIFFRACTIONp_staggered_tor23.415
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.520
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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