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- PDB-1oah: Cytochrome c Nitrite Reductase from Desulfovibrio desulfuricans A... -

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Basic information

Entry
Database: PDB / ID: 1oah
TitleCytochrome c Nitrite Reductase from Desulfovibrio desulfuricans ATCC 27774: The relevance of the two calcium sites in the structure of the catalytic subunit (NrfA).
ComponentsCYTOCHROME C NITRITE REDUCTASE
KeywordsREDUCTASE / CYTOCHROME C / NITRITE REDUCTASE / NITROGEN CYCLE / RESPIRATORY NITRITE AMMONIFICATION
Function / homology
Function and homology information


nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / anaerobic electron transport chain / outer membrane-bounded periplasmic space / heme binding / metal ion binding
Similarity search - Function
Cytochrome c552 / Cytochrome c552 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Multiheme cytochrome superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Prokaryotic membrane lipoprotein lipid attachment site profile. / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / nitrite reductase (cytochrome; ammonia-forming)
Similarity search - Component
Biological speciesDESULFOVIBRIO DESULFURICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD, molecular replacement / Resolution: 2.3 Å
AuthorsCunha, C.A. / Macieira, S. / Dias, J.M. / Almeida, G. / Goncalves, L.L. / Costa, C. / Lampreia, J. / Huber, R. / Moura, J.J.G. / Moura, I. / Romao, M.J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Cytochrome C Nitrite Reductase from Desulfovibrio Desulfuricans Atcc 27774. The Relevance of the Two Calcium Sites in the Structure of the Catalytic Subunit (Nrfa)
Authors: Cunha, C.A. / Macieira, S. / Dias, J.M. / Almeida, G. / Goncalves, L.L. / Costa, C. / Lampreia, J. / Huber, R. / Moura, J.J.G. / Moura, I. / Romao, M.J.
History
DepositionJan 14, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Sep 25, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Experimental preparation / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / exptl_crystal_grow / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
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_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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.id
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C NITRITE REDUCTASE
B: CYTOCHROME C NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,08322
Polymers118,4652
Non-polymers6,61820
Water8,989499
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)78.940, 104.600, 143.180
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, 2 molecules AB

#1: Protein CYTOCHROME C NITRITE REDUCTASE


Mass: 59232.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO DESULFURICANS (bacteria)
References: UniProt: Q8VNU2, nitrite reductase (cytochrome; ammonia-forming)

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Non-polymers , 5 types, 519 molecules

#2: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 499 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsRESIDUE 519 PRESENT IN THE ELECTRON DENSITY NOT SEQUENCE

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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: 2.34 Å3/Da / Density % sol: 47 %
Description: THE STRUCTURE WAS SOLVED COMBINING MAD PHASES WITH A MOLECULAR REPLACEMENT SOLUTION. THE MAD DATA SET (TO 2.5 ANGSTROMS RESOLUTION) WAS COLLECTED AT BEAMLINE BM14 WITH A MAR345 DETECTOR ...Description: THE STRUCTURE WAS SOLVED COMBINING MAD PHASES WITH A MOLECULAR REPLACEMENT SOLUTION. THE MAD DATA SET (TO 2.5 ANGSTROMS RESOLUTION) WAS COLLECTED AT BEAMLINE BM14 WITH A MAR345 DETECTOR AND A DATASET UP TO 2.3 ANGSTROMS WAS COLLECTED AT ID14-EH4 WITH A ADSC DETECTOR.
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 15% W/V PEG 3350, CACL2 0.2M, HEPES PH7.5, 0.1M, 3-(DECYL-METHYLAMMONIUM)PROPANE-1-SULFONATE (ZWITTERGENT 3-10) AS ADDITIVE, pH 7.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
115 %(w/v)PEG33501reservoir
20.2 M1reservoirCaCl2
30.1 MHEPES1reservoirpH7.5
410 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.7403,1.7390,0.9919, 0.932
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.74031
21.7391
30.99191
40.9321
ReflectionResolution: 2.3→84.5 Å / Num. obs: 53690 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.2 / % possible all: 89.8
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. obs: 51633 / % possible obs: 97.3 %
Reflection shell
*PLUS
% possible obs: 89.8 %

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
SHARPFOR MADphasing
AMoREFOR MRphasing
RefinementMethod to determine structure: MAD, molecular replacement
Starting model: PDB ENTRY 1QDB

1qdb


Resolution: 2.3→20 Å / SU B: 6.381 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.313 / ESU R Free: 0.214
Details: RESIDUES 325 - 331 ARE MISSING IN CHAIN A BECAUSE NO ELECTRON DENSITY CORRESPONDING TO THESE RESIDUES COULD BE SEEN IN THE ELECTRON DENSITY MAPS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 522 1 %RANDOM
Rwork0.189 ---
obs-51633 97.3 %-
Displacement parametersBiso mean: 27.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.28 Å20 Å20 Å2
2--1.03 Å20 Å2
3----2.31 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7705 0 440 499 8644
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.378

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