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- PDB-7p2f: Green-type copper-nitrite reductase from Sinorhizobium meliloti 2011 -

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Basic information

Entry
Database: PDB / ID: 7p2f
TitleGreen-type copper-nitrite reductase from Sinorhizobium meliloti 2011
ComponentsCopper-containing nitrite reductase
KeywordsMETAL BINDING PROTEIN / Nitrite reductase / Denitrification pathway / Greek key B-barrel domains
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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesSinorhizobium meliloti 2011 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTolmie, C. / Opperman, D.J. / Ferroni, F.M.
Funding support Argentina, South Africa, United Kingdom, 5items
OrganizationGrant numberCountry
National Scientific and Technical Research Council (CONICET)11220150110550CO Argentina
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)PICT2017-2186 Argentina
National Research Foundation in South Africa96087 South Africa
National Research Foundation in South Africa132477 South Africa
Global Challenges Research FundST/R002754/1 United Kingdom
CitationJournal: Protein Sci. / Year: 2021
Title: Copper nitrite reductase from Sinorhizobium meliloti 2011: Crystal structure and interaction with the physiological versus a nonmetabolically related cupredoxin-like mediator.
Authors: Ramirez, C.S. / Tolmie, C. / Opperman, D.J. / Gonzalez, P.J. / Rivas, M.G. / Brondino, C.D. / Ferroni, F.M.
History
DepositionJul 5, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 27, 2021Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
B: Copper-containing nitrite reductase
C: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,2889
Polymers120,9073
Non-polymers3816
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12820 Å2
ΔGint-88 kcal/mol
Surface area32860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.430, 215.390, 114.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Copper-containing nitrite reductase


Mass: 40302.363 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti 2011 (bacteria) / Gene: nirK, GHL01_01400 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q5SEZ8, nitrite reductase (NO-forming)
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.17 Å3/Da / Density % sol: 61.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2 M MgCl2, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jan 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.5→78.58 Å / Num. obs: 52802 / % possible obs: 98.9 % / Redundancy: 5.7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.057 / Rrim(I) all: 0.139 / Net I/σ(I): 9.4
Reflection shellResolution: 2.5→2.58 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.86 / Num. unique obs: 4453 / CC1/2: 0.675 / Rpim(I) all: 0.424 / Rrim(I) all: 0.963 / % possible all: 97.3

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Processing

Software
NameVersionClassification
Aimless0.5.1data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AQ8

1aq8


Resolution: 2.5→78.58 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.897 / SU ML: 0.184 / SU R Cruickshank DPI: 0.2927 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.293 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2243 2587 4.9 %RANDOM
Rwork0.1817 ---
obs0.1839 50185 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.24 Å2 / Biso mean: 38.279 Å2 / Biso min: 5.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0 Å2-0 Å2
2---0.03 Å2-0 Å2
3---0.1 Å2
Refinement stepCycle: final / Resolution: 2.5→78.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7511 0 6 187 7704
Biso mean--36.4 31.85 -
Num. residues----985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0137736
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177112
X-RAY DIFFRACTIONr_angle_refined_deg1.4851.64210517
X-RAY DIFFRACTIONr_angle_other_deg1.1351.57716387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.145982
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77423.361366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.821151151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1051527
X-RAY DIFFRACTIONr_chiral_restr0.0550.2998
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021732
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 139 -
Rwork0.325 3645 -
all-3784 -
obs--96.38 %

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