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- PDB-2a3t: Cu-containing nitrite reductase -

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Basic information

Entry
Database: PDB / ID: 2a3t
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: 1.85 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 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 7, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Aug 23, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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
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
Water4,252236
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 area13690 Å2
ΔGint-126 kcal/mol
Surface area31570 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)72.436, 72.436, 148.089
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-672-

HOH

DetailsThe biological unit is a trimer and can be generated from the monomer in the asymmetric unit by applying the symmetry 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 / Copper


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 / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.4
Details: PEG 4000, 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: 1.017 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 28, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.017 Å / Relative weight: 1
ReflectionResolution: 1.85→36.2 Å / Num. all: 24723 / Num. obs: 24723 / % possible obs: 100 % / Rmerge(I) obs: 0.079
Reflection shellResolution: 1.85→1.92 Å / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4.1 / Num. unique all: 2472 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB: 1ZV2

1zv2


Resolution: 1.85→18.5 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.454 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.17627 1257 5.1 %RANDOM
Rwork0.14881 ---
all0.15022 23444 --
obs0.15022 23444 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.504 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.32 Å20 Å2
2---0.65 Å20 Å2
3---0.97 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.114 Å0.133 Å
Refinement stepCycle: LAST / Resolution: 1.85→18.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2522 0 5 236 2763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212599
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.9513541
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8445327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.36124.237118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.21515395
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2231511
X-RAY DIFFRACTIONr_chiral_restr0.1130.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022035
X-RAY DIFFRACTIONr_nbd_refined0.1980.21113
X-RAY DIFFRACTIONr_nbtor_refined0.310.21726
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2233
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.234
X-RAY DIFFRACTIONr_mcbond_it0.9321.51680
X-RAY DIFFRACTIONr_mcangle_it1.35322623
X-RAY DIFFRACTIONr_scbond_it2.21931051
X-RAY DIFFRACTIONr_scangle_it3.4654.5918
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.209 105 -
Rwork0.18 1712 -
obs--99.94 %

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