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- PDB-2zoo: Crystal structure of nitrite reductase from Pseudoalteromonas hal... -

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Basic information

Entry
Database: PDB / ID: 2zoo
TitleCrystal structure of nitrite reductase from Pseudoalteromonas haloplanktis TAC125
ComponentsProbable nitrite reductase
KeywordsOXIDOREDUCTASE / nitrite / electron transfer / Electron transport / Heme / Iron / Metal-binding / Transport
Function / homology
Function and homology information


denitrification pathway / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / nitrate assimilation / periplasmic space / electron transfer activity / copper ion binding / heme binding
Similarity search - Function
: / Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Cytochrome c / Multicopper oxidase / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins ...: / Nitrite reductase, copper-type / Multicopper oxidase, type 1 / Cytochrome c / Multicopper oxidase / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxins - blue copper proteins / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Cupredoxin / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
sucrose / COPPER (II) ION / PROTOPORPHYRIN IX CONTAINING FE / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesPseudoalteromonas haloplanktis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsNojiri, M. / Tsuda, A. / Yamaguchi, K. / Suzuki, S.
CitationJournal: To be Published
Title: Electron transfer processes within and between proteins containing the HEME C and blue Cu
Authors: Nojiri, M. / Koteishi, H. / Tsuda, A. / Nakagami, T. / Kobayashi, K. / Inoue, T. / Yamaguchi, K. / Suzuki, S.
History
DepositionMay 27, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9948
Polymers47,6201
Non-polymers1,3747
Water7,242402
1
A: Probable nitrite reductase
hetero molecules

A: Probable nitrite reductase
hetero molecules

A: Probable nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,98324
Polymers142,8613
Non-polymers4,12221
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area27470 Å2
ΔGint-240 kcal/mol
Surface area42600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)180.338, 180.338, 180.338
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-1054-

HOH

21A-1139-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Probable nitrite reductase


Mass: 47620.258 Da / Num. of mol.: 1 / Fragment: UNP residues 26-467 / Source method: isolated from a natural source / Source: (natural) Pseudoalteromonas haloplanktis (bacteria) / Strain: TAC125
References: UniProt: Q3IGF7, EC: 1.7.99.3, nitrite reductase (NO-forming)
#2: Polysaccharide beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 408 molecules

#3: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 402 / 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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Lithium sulfate, Ammonium sulfate, Sodium citrate, Sucrose, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Sep 29, 2007
RadiationMonochromator: double crystals Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.95→43.8 Å / Num. all: 72995 / Num. obs: 72995 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.95→2.02 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1kbw, 1c52

1kbw

1c52


Resolution: 1.95→8 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.967 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18604 7167 10.1 %RANDOM
Rwork0.16564 ---
obs0.16769 63885 99.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.22 Å2
Refinement stepCycle: LAST / Resolution: 1.95→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3326 0 83 402 3811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223489
X-RAY DIFFRACTIONr_angle_refined_deg1.5192.0024766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.965437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9925.414157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.45415527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4191511
X-RAY DIFFRACTIONr_chiral_restr0.1270.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022693
X-RAY DIFFRACTIONr_nbd_refined0.2220.21614
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22389
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2323
X-RAY DIFFRACTIONr_metal_ion_refined0.0650.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1910.2153
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.274
X-RAY DIFFRACTIONr_mcbond_it0.9931.52226
X-RAY DIFFRACTIONr_mcangle_it1.36523497
X-RAY DIFFRACTIONr_scbond_it2.33431418
X-RAY DIFFRACTIONr_scangle_it3.6434.51267
LS refinement shellResolution: 1.952→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 522 -
Rwork0.208 4436 -
obs--99.26 %

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