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- PDB-1j9r: Crystal structure of nitrite soaked reduced D98N AFNIR -

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Basic information

Entry
Database: PDB / ID: 1j9r
TitleCrystal structure of nitrite soaked reduced D98N AFNIR
ComponentsCOPPER-CONTAINING NITRITE REDUCTASE
KeywordsOXIDOREDUCTASE / curpredoxin fold copper nitrite
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 speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsBoulanger, M.J. / Murphy, M.E.
CitationJournal: Biochemistry / Year: 2001
Title: Alternate substrate binding modes to two mutant (D98N and H255N) forms of nitrite reductase from Alcaligenes faecalis S-6: structural model of a transient catalytic intermediate
Authors: Boulanger, M.J. / Murphy, M.E.
History
DepositionMay 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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.ptnr2_auth_asym_id / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)111,34315
Polymers110,6333
Non-polymers71012
Water19,7981099
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13270 Å2
ΔGint-95 kcal/mol
Surface area32980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.436, 102.319, 145.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein COPPER-CONTAINING NITRITE REDUCTASE / CU-NIR


Mass: 36877.664 Da / Num. of mol.: 3 / Fragment: RESIDUES 40-376 / Mutation: D98N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Strain: S-6 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174 DE3 / References: UniProt: P38501, EC: 1.7.99.3
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1099 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 6000, sodium acetate, sodium nitrite, copper chloride, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 Msodium cacodylate1reservoir
20.1 Msodium acetate1reservoir
310-15 %PEG60001reservoir
45 mM1reservoirequimolarCuCl2
55 mMzinc acetate1reservoirequimolar
610 mg/mlprotein1drop
710 mMTris1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Mar 12, 2000 / Details: osmic mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 62966 / Num. obs: 61451 / % possible obs: 97.6 % / Redundancy: 9.6 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.6
Reflection shellResolution: 2→2.13 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.143 / Mean I/σ(I) obs: 4.25 / % possible all: 95.5
Reflection
*PLUS
Lowest resolution: 50 Å / Redundancy: 9.68 %
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 95.5 % / Num. unique obs: 9867 / Rmerge(I) obs: 0.294

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→50 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2694644.45 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.225 6233 10.2 %RANDOM
Rwork0.186 ---
all0.186 62945 --
obs0.186 61394 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.22 Å2 / ksol: 0.365 e/Å3
Displacement parametersBiso mean: 27.9 Å2
Baniso -1Baniso -2Baniso -3
1-6.47 Å20 Å20 Å2
2---1.23 Å20 Å2
3----5.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7680 0 18 1099 8797
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_mcbond_it0.321.5
X-RAY DIFFRACTIONc_mcangle_it0.62
X-RAY DIFFRACTIONc_scbond_it1.012
X-RAY DIFFRACTIONc_scangle_it1.222.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 965 9.8 %
Rwork0.222 8859 -
obs--95 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAM_EH.CUTOPOLOGY_EH.CU
Software
*PLUS
Name: CNS / Version: 0.4 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.92
X-RAY DIFFRACTIONc_mcbond_it0.321.5
X-RAY DIFFRACTIONc_scbond_it1.012
X-RAY DIFFRACTIONc_mcangle_it0.62
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.262 / % reflection Rfree: 9.8 % / Rfactor Rwork: 0.222

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