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- PDB-2dwt: Cu-containing nitrite reductase at pH 6.0 with bound nitrite -

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Basic information

Entry
Database: PDB / ID: 2dwt
TitleCu-containing nitrite reductase at pH 6.0 with bound nitrite
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 / NITRITE ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionAug 17, 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 1.3Oct 11, 2017Group: Advisory / Data collection / Refinement description
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.name
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_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 / _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

Downloads & links

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1315
Polymers35,9121
Non-polymers2194
Water1,874104
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)108,39215
Polymers107,7353
Non-polymers65712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area14440 Å2
ΔGint-97 kcal/mol
Surface area31180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.740, 74.740, 153.146
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-532-

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 / Copper


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.29 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: Tris, MgCl2, NaNO2, PEG 4000, 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: I711 / Wavelength: 1.063
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 27, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.063 Å / Relative weight: 1
ReflectionResolution: 1.9→24.71 Å / Num. obs: 24972 / % possible obs: 99.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 7.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-23.10.3631.81150436640.363100
2-2.123.20.2333.21104435030.233100
2.12-2.273.20.1594.61033432650.15999.9
2.27-2.453.20.1136.4961130200.11399.8
2.45-2.693.20.0957.1896827960.09599.5
2.69-33.20.0689808925030.06899.3
3-3.473.20.0511.5718122120.0599
3.47-4.253.30.04113.1603118400.04198.5
4.25-6.013.30.04611.8471714220.04697.7
6.01-37.373.20.03517.224157470.03593.6

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZV2

1zv2


Resolution: 1.9→24.71 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.192 / SU ML: 0.123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.171 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1270 5.1 %RANDOM
Rwork0.199 ---
all0.201 ---
obs-24965 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.106 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å2-0.78 Å20 Å2
2---1.55 Å20 Å2
3---2.33 Å2
Refinement stepCycle: LAST / Resolution: 1.9→24.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2530 0 8 104 2642
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212571
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.9483505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6425328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.70724.054111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44415374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5641510
X-RAY DIFFRACTIONr_chiral_restr0.1330.2379
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022010
X-RAY DIFFRACTIONr_nbd_refined0.2130.21134
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21697
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2150
X-RAY DIFFRACTIONr_metal_ion_refined0.0320.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.282
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.226
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.040.21
X-RAY DIFFRACTIONr_mcbond_it1.1311.51696
X-RAY DIFFRACTIONr_mcangle_it1.62222623
X-RAY DIFFRACTIONr_scbond_it2.50731020
X-RAY DIFFRACTIONr_scangle_it3.3044.5882
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 82 -
Rwork0.253 1812 -
obs-1894 100 %

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