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- PDB-1zv2: Cu-containing nitrite reductase -

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Basic information

Entry
Database: PDB / ID: 1zv2
TitleCu-containing nitrite reductase
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / copper protein / nitrite reduction / denitrification
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, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like ...Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsJacobson, F. / Guo, H. / Olesen, K. / Okvist, M. / Neutze, R. / Sjolin, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structures of the oxidized and reduced forms of nitrite reductase from Rhodobacter sphaeroides 2.4.3 at high pH: changes in the interactions of the type 2 copper.
Authors: Jacobson, F. / Guo, H. / Olesen, K. / Okvist, M. / Neutze, R. / Sjolin, L.
History
DepositionJun 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.4Aug 23, 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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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.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
Remark 999SEQUENCE The author states that residues ASP 230, ASN 281, SER 319, HIS 351, VAL 367, ALA 368 are ...SEQUENCE The author states that residues ASP 230, ASN 281, SER 319, HIS 351, VAL 367, ALA 368 are correct based on the electron density.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9986
Polymers35,7981
Non-polymers2005
Water5,314295
1
A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules

A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,99518
Polymers107,3953
Non-polymers60015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area13650 Å2
ΔGint-129 kcal/mol
Surface area31160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.381, 72.381, 147.509
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-636-

HOH

21A-700-

HOH

31A-770-

HOH

41A-786-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -y, x-y, z and -x+y, -x, z.

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Components

#1: Protein Copper-containing nitrite reductase / Cu-NIR


Mass: 35798.488 Da / Num. of mol.: 1 / Fragment: residues 44-371
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Gene: nirK / Plasmid: pET17b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53239, 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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 3.1 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: PEG4000, MgCl2, Tris, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.007 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 28, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.007 Å / Relative weight: 1
ReflectionResolution: 1.74→26.7 Å / Num. obs: 29034 / % possible obs: 98.6 % / Observed criterion σ(I): -3.7 / Rmerge(I) obs: 0.065 / Net I/σ(I): 9.7
Reflection shellResolution: 1.74→1.81 Å / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 2.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NIF

1nif


Resolution: 1.74→26.7 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.002 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.19367 1465 5 %RANDOM
Rwork0.1547 ---
obs0.15667 27569 97.64 %-
all-27569 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.943 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.111 Å0.116 Å
Refinement stepCycle: LAST / Resolution: 1.74→26.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 5 295 2822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212615
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4381.953567
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9775331
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41924.25120
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.03315397
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8521511
X-RAY DIFFRACTIONr_chiral_restr0.0990.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022053
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.21185
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.21742
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2253
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0720.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.2106
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.252
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7761.51688
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14722636
X-RAY DIFFRACTIONr_scbond_it2.0331062
X-RAY DIFFRACTIONr_scangle_it3.0714.5929
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.737→1.782 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 94 -
Rwork0.19 1822 -
obs--86.54 %

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