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- PDB-2dy2: Nitrite reductase pH 6.0 -

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Basic information

Entry
Database: PDB / ID: 2dy2
TitleNitrite reductase pH 6.0
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / copper protein / cupredoxin / 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: 2.26 Å
AuthorsJacobson, F.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: pH Dependence of Copper Geometry, Reduction Potential, and Nitrite Affinity in Nitrite Reductase
Authors: Jacobson, F. / Pistorius, A. / Farkas, D. / De Grip, W. / Hansson, O. / Sjolin, L. / Neutze, R.
History
DepositionSep 5, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 23, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn_source.pdbx_synchrotron_site / _diffrn_source.pdbx_wavelength / _diffrn_source.pdbx_wavelength_list
Revision 1.4Oct 25, 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

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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)36,0393
Polymers35,9121
Non-polymers1272
Water1,29772
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)108,1169
Polymers107,7353
Non-polymers3816
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 area13600 Å2
ΔGint-95 kcal/mol
Surface area31180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.996, 74.996, 153.611
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-439-

HOH

DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -y, x-y-1, z-1 and -x+y, -x-1, z-l.

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Components

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


Mass: 35911.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides (bacteria) / Strain: 2.4.3 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.31 Å3/Da / Density % sol: 46.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Tris, MgCl2, PEG 1500, pH 6.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1.115 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115 Å / Relative weight: 1
ReflectionResolution: 2.26→31.77 Å / Num. obs: 15045 / % possible obs: 99.8 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 7.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.26-2.385.60.2942.61215721740.294100
2.38-2.535.60.2073.71185921090.207100
2.53-2.75.60.1614.61093819480.161100
2.7-2.925.70.11461045118470.114100
2.92-3.25.70.0788.4939916570.078100
3.2-3.575.70.06310.1877115510.063100
3.57-4.135.70.04911.8739313030.049100
4.13-5.055.70.04512.6652011430.045100
5.05-7.155.70.05311.449908730.053100
7.15-51.235.20.03320.423004400.03392.1

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZV2

1zv2


Resolution: 2.26→31.77 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.93 / SU B: 7.59 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.361 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.241 760 5.1 %RANDOM
Rwork0.192 ---
all0.194 ---
obs-15043 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.279 Å2
Baniso -1Baniso -2Baniso -3
1--2.07 Å2-1.04 Å20 Å2
2---2.07 Å20 Å2
3---3.11 Å2
Refinement stepCycle: LAST / Resolution: 2.26→31.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 2 72 2604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212599
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.9523543
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4835328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.62324.188117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.03815391
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6141511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022035
X-RAY DIFFRACTIONr_nbd_refined0.2070.21112
X-RAY DIFFRACTIONr_nbtor_refined0.3090.21686
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2150
X-RAY DIFFRACTIONr_metal_ion_refined0.0030.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.285
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.226
X-RAY DIFFRACTIONr_mcbond_it0.7481.51680
X-RAY DIFFRACTIONr_mcangle_it1.27922628
X-RAY DIFFRACTIONr_scbond_it1.77531047
X-RAY DIFFRACTIONr_scangle_it2.6644.5915
LS refinement shellResolution: 2.26→2.319 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 60 -
Rwork0.252 1049 -
obs-1109 100 %

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