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- PDB-2dv6: Crystal structure of nitrite reductase from Hyphomicrobium denitr... -

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Basic information

Entry
Database: PDB / ID: 2dv6
TitleCrystal structure of nitrite reductase from Hyphomicrobium denitrificans
ComponentsNitrite reductase
KeywordsOXIDOREDUCTASE / nitrite / electron transfer / reduction / denitrification
Function / homology
Function and homology information


nitrite reductase (NO-forming) / : / nitrite reductase (NO-forming) activity / copper ion binding / identical protein binding
Similarity search - Function
Nitrite reductase, copper-type / 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 speciesHyphomicrobium denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNojiri, M. / Xie, Y. / Yamamoto, T. / Inoue, T. / Suzuki, S. / Kai, Y.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: Structure and function of a hexameric copper-containing nitrite reductase.
Authors: Nojiri, M. / Xie, Y. / Inoue, T. / Yamamoto, T. / Matsumura, H. / Kataoka, K. / Deligeer / Yamaguchi, K. / Kai, Y. / Suzuki, S.
History
DepositionJul 28, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / 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_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_alt_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_alt_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.pdbx_ptnr2_label_alt_id / _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_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
B: Nitrite reductase
C: Nitrite reductase
D: Nitrite reductase
E: Nitrite reductase
F: Nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)290,71030
Polymers289,3326
Non-polymers1,37824
Water32,4271800
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33550 Å2
ΔGint-265 kcal/mol
Surface area77270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.551, 162.551, 148.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Nitrite reductase /


Mass: 48221.965 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Hyphomicrobium denitrificans (bacteria) / Strain: A3151 / References: UniProt: Q8KKH4, nitrite reductase (NO-forming)
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1800 / 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: 3.4 Å3/Da / Density % sol: 63.81 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG4000, potassium thiocyanate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: May 19, 2005
RadiationMonochromator: double crystals Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→48.59 Å / Num. all: 195178 / Num. obs: 195178 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.2→2.28 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1kbw

1kbw


Resolution: 2.2→8 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.9 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1653 9588 5 %RANDOM
Rwork0.15164 ---
obs0.15233 180940 99.77 %-
all-194626 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.525 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.1 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19260 0 24 1803 21087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02219734
X-RAY DIFFRACTIONr_angle_refined_deg1.8391.9526856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.55252526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.76924.11876
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.119153012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2641596
X-RAY DIFFRACTIONr_chiral_restr0.1720.22988
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215288
X-RAY DIFFRACTIONr_nbd_refined0.2230.29423
X-RAY DIFFRACTIONr_nbtor_refined0.3130.213104
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.21978
X-RAY DIFFRACTIONr_metal_ion_refined0.3670.243
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.234
X-RAY DIFFRACTIONr_mcbond_it0.8481.512504
X-RAY DIFFRACTIONr_mcangle_it1.574220232
X-RAY DIFFRACTIONr_scbond_it2.44137266
X-RAY DIFFRACTIONr_scangle_it3.934.56624
LS refinement shellResolution: 2.202→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.216 687 -
Rwork0.196 12555 -
obs--99.46 %

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