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- PDB-1npj: Crystal structure of H145A mutant of nitrite reductase from Alcal... -

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Basic information

Entry
Database: PDB / ID: 1npj
TitleCrystal structure of H145A mutant of nitrite reductase from Alcaligenes faecalis
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / copper nitrite reductase
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 speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWijma, H.J. / Boulanger, M.J. / Molon, A. / Fittipaldi, M. / Huber, M. / Murphy, M.E. / Verbeet, M.P. / Canters, G.W.
CitationJournal: Biochemistry / Year: 2003
Title: Reconstitution of the type-1 active site of the H145G/A variants of nitrite reductase by ligand insertion
Authors: Wijma, H.J. / Boulanger, M.J. / Molon, A. / Fittipaldi, M. / Huber, M. / Murphy, M.E. / Verbeet, M.P. / Canters, G.W.
History
DepositionJan 18, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 3, 2018Group: Advisory / Data collection / Category: pdbx_unobs_or_zero_occ_residues
Revision 1.4Oct 27, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / 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 1.5Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)111,3729
Polymers110,9903
Non-polymers3816
Water22,5371251
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13140 Å2
ΔGint-134 kcal/mol
Surface area33130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.600, 102.520, 146.070
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: 36996.820 Da / Num. of mol.: 3 / Mutation: H145A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: NIRK OR NIR / Plasmid: pet28a / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174DE3 / References: UniProt: P38501, EC: 1.7.99.3
#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.: 1251 / 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: 1.85 Å3/Da / Density % sol: 32.86 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 8000, sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.1 Msodium cacodylate1reservoirpH5.5
20.1 Msodium acetate1reservoirpH4.7
32 mMzinc acetate1reservoir
42 mM1reservoirpH5.5CoCl2
58-12 %PEG6001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Oct 10, 2001 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 73819 / Num. obs: 64626 / % possible obs: 87.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 17.9 Å2
Reflection shellResolution: 1.9→2.05 Å / Mean I/σ(I) obs: 4 / % possible all: 86
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Rmerge(I) obs: 0.088
Reflection shell
*PLUS
Highest resolution: 1.9 Å / % possible obs: 86 % / Num. unique obs: 12511 / Rmerge(I) obs: 0.261 / Mean I/σ(I) obs: 4.65

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J9Q

1j9q


Resolution: 1.9→31.41 Å / Data cutoff high absF: 2190210.08 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.225 3682 -RANDOM
Rwork0.177 ---
all-736 --
obs-64538 87.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.8665 Å2 / ksol: 0.335529 e/Å3
Displacement parametersBiso mean: 26.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.25 Å20 Å20 Å2
2--1.82 Å20 Å2
3----7.07 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→31.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7665 0 6 1251 8922
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.692
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.612.5
LS refinement shellResolution: 1.9→2.02 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.225 10422 -
obs--86.1 %
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
Refinement
*PLUS
Rfactor Rwork: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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