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- PDB-5b1j: Crystal structure of the electron-transfer complex of copper nitr... -

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Basic information

Entry
Database: PDB / ID: 5b1j
TitleCrystal structure of the electron-transfer complex of copper nitrite reductase with a cupredoxin
Components
  • Blue copper proteinCopper protein
  • Copper-containing nitrite reductase
KeywordsOXIDOREDUCTASE/ELECTRON TRANSPORT / complex / copper nitrite reductase / electron transfer / OXIDOREDUCTASE-ELECTRON TRANSPORT complex
Function / homology
Function and homology information


denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / electron transfer activity / copper ion binding
Similarity search - Function
Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / Nitrite reductase, copper-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal ...Pseudoazurin / Amicyanin/Pseudoazurin / Blue (type 1) copper protein, plastocyanin-type / Nitrite reductase, copper-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / 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 / Blue copper protein / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAlcaligenes xylosoxydans xylosoxydans (bacteria)
Hyphomicrobium denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsNojiri, M. / Koteishi, H. / Yoneda, R. / Hira, D.
CitationBook title: Metalloenzymes in denitrification: Applications and Environmental impacts
Journal: Metalloenzymes in denitrification: Applications and Environmental impacts
Year: 2016
Title: Structure and Function of Copper Nitrite Reductase
Authors: Nojiri, M.
History
DepositionDec 4, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
B: Copper-containing nitrite reductase
C: Blue copper protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0498
Polymers86,7323
Non-polymers3185
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-25 kcal/mol
Surface area35600 Å2
Unit cell
Length a, b, c (Å)153.226, 153.226, 153.226
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Copper-containing nitrite reductase / Dissimilatory copper-containing nitrite reductase / Nitrite Reductase (NiR)


Mass: 36570.527 Da / Num. of mol.: 2 / Fragment: UNP residues 25-360 / Source method: isolated from a natural source
Source: (natural) Alcaligenes xylosoxydans xylosoxydans (bacteria)
References: UniProt: O68601, nitrite reductase (NO-forming)
#2: Protein Blue copper protein / Copper protein / pseudoazurin


Mass: 13590.666 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hyphomicrobium denitrificans (bacteria) / References: UniProt: A7VL37
#3: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cu

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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: 3.46 Å3/Da / Density % sol: 64.42 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, potassium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jan 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3→19.1 Å / Num. obs: 23931 / % possible obs: 99.2 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 18.7
Reflection shellResolution: 3→3.05 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1oe1

1oe1


Resolution: 3→19.1 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.908 / SU B: 15.431 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R Free: 0.369 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23279 1217 5.1 %RANDOM
Rwork0.17135 ---
obs0.17453 22698 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.345 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 3→19.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6050 0 5 0 6055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0196210
X-RAY DIFFRACTIONr_bond_other_d0.0010.025889
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9518446
X-RAY DIFFRACTIONr_angle_other_deg0.817313596
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8925789
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60724.672259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.8715988
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2731521
X-RAY DIFFRACTIONr_chiral_restr0.0820.2929
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217047
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021364
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_it3.2835.2063165
X-RAY DIFFRACTIONr_mcbond_other3.2815.2053164
X-RAY DIFFRACTIONr_mcangle_it5.1827.8023951
X-RAY DIFFRACTIONr_mcangle_other5.1837.8033952
X-RAY DIFFRACTIONr_scbond_it3.2095.463045
X-RAY DIFFRACTIONr_scbond_other3.2095.463045
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1118.0694495
X-RAY DIFFRACTIONr_long_range_B_refined7.24141.1616715
X-RAY DIFFRACTIONr_long_range_B_other7.24141.1656716
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.003→3.081 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 82 -
Rwork0.267 1690 -
obs--99.16 %

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