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- PDB-2ppd: Oxidized H145A mutant of AfNiR bound to nitric oxide -

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Basic information

Entry
Database: PDB / ID: 2ppd
TitleOxidized H145A mutant of AfNiR bound to nitric oxide
ComponentsCopper-containing nitrite reductase
KeywordsOXIDOREDUCTASE / H145A / nitrite reductase / nitric oxide / denitrification / bacteria
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
ACETATE ION / COPPER (II) ION / COPPER (I) ION / NITRIC OXIDE / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesAlcaligenes faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTocheva, E.I. / Murphy, M.E.P.
CitationJournal: Biochemistry / Year: 2007
Title: Stable copper-nitrosyl formation by nitrite reductase in either oxidation state
Authors: Tocheva, E.I. / Rosell, F.I. / Mauk, A.G. / Murphy, M.E.
History
DepositionApr 28, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 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.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 1.3Feb 21, 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)111,61313
Polymers110,9903
Non-polymers62210
Water10,863603
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14170 Å2
ΔGint-140 kcal/mol
Surface area32950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.957, 102.062, 145.797
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

#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) / Strain: S-6 / Gene: nirK, nir / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P38501, nitrite reductase (NO-forming)

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Non-polymers , 6 types, 613 molecules

#2: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 603 / 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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 6-11% polyethylene glycol 6000, 0.1 M ammonium sulfate and 0.01 M sodium acetate buffer, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 85250 / Redundancy: 3.4 % / Rmerge(I) obs: 0.055
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.522

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→83.62 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.878 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21228 4208 5 %RANDOM
Rwork0.18799 ---
obs0.18922 79536 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.926 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å20 Å2
2---0.05 Å20 Å2
3----1.31 Å2
Refinement stepCycle: LAST / Resolution: 1.8→83.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7672 0 21 603 8296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227966
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.94710845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77151018
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.84624.692341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.839151196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4031523
X-RAY DIFFRACTIONr_chiral_restr0.0890.21192
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026169
X-RAY DIFFRACTIONr_nbd_refined0.1890.23602
X-RAY DIFFRACTIONr_nbtor_refined0.3080.25314
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1060.2674
X-RAY DIFFRACTIONr_metal_ion_refined0.0790.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.286
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.227
X-RAY DIFFRACTIONr_mcbond_it0.7161.55180
X-RAY DIFFRACTIONr_mcangle_it1.08628120
X-RAY DIFFRACTIONr_scbond_it1.74833178
X-RAY DIFFRACTIONr_scangle_it2.6274.52725
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 297 -
Rwork0.267 5700 -
obs--96.41 %

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