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- PDB-1zds: Crystal Structure of Met150Gly AfNiR with Acetamide Bound -

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Basic information

Entry
Database: PDB / ID: 1zds
TitleCrystal Structure of Met150Gly AfNiR with Acetamide Bound
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / Metal-binding / Nitrate assimiliation
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
ACETAMIDE / COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.55 Å
AuthorsWijma, H.J. / MacPherson, I.S. / Alexandre, M. / Diederix, R.E.M. / Canters, G.W. / Murphy, M.E.P. / Verbeet, M.P.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: A rearranging ligand enables allosteric control of catalytic activity in copper-containing nitrite reductase.
Authors: Wijma, H.J. / Macpherson, I. / Alexandre, M. / Diederix, R.E. / Canters, G.W. / Murphy, M.E. / Verbeet, M.P.
History
DepositionApr 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 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 14, 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)109,47615
Polymers108,7413
Non-polymers73612
Water20,5911143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14450 Å2
ΔGint-88 kcal/mol
Surface area32870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.645, 102.365, 146.189
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: 36246.883 Da / Num. of mol.: 3 / Mutation: M150G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alcaligenes faecalis (bacteria) / Gene: nirK, nir / References: UniProt: P38501, nitrite reductase (NO-forming)
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ACM / ACETAMIDE / Acetamide


Mass: 59.067 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H5NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1143 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.46 %

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Data collection

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.55→84.52 Å / Num. all: 102891

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Processing

SoftwareName: REFMAC / Version: 5.1.24 / Classification: refinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.55→84.52 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.313 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21388 5439 5 %RANDOM
Rwork0.18178 ---
all0.183 ---
obs0.18339 102891 80.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.865 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å20 Å20 Å2
2---0.4 Å20 Å2
3----2.29 Å2
Refinement stepCycle: LAST / Resolution: 1.55→84.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7666 0 30 1143 8839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0217897
X-RAY DIFFRACTIONr_bond_other_d0.0020.026988
X-RAY DIFFRACTIONr_angle_refined_deg1.2211.9410763
X-RAY DIFFRACTIONr_angle_other_deg0.762316288
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.19851004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0760.21178
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028963
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021538
X-RAY DIFFRACTIONr_nbd_refined0.1880.21333
X-RAY DIFFRACTIONr_nbd_other0.2380.28350
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0790.24536
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2861
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.265
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5091.55002
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.90928045
X-RAY DIFFRACTIONr_scbond_it1.38532895
X-RAY DIFFRACTIONr_scangle_it2.2574.52718
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.378 248
Rwork0.391 4901

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