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- PDB-1h9y: Cytochrome cd1 Nitrite Reductase, reduced form complexed to CN -

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Basic information

Entry
Database: PDB / ID: 1h9y
TitleCytochrome cd1 Nitrite Reductase, reduced form complexed to CN
ComponentsCYTOCHROME CD1 NITRITE REDUCTASE
KeywordsOXIDOREDUCTASE / ENZYME / NITRITE REDUCTASE / CN
Function / homology
Function and homology information


hydroxylamine reductase / hydroxylamine reductase activity / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase / Cytochrome cd1-nitrite reductase, C-terminal domain superfamily / Cytochrome D1 heme domain / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / 8 Propeller / Methanol Dehydrogenase; Chain A / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. ...C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase / Cytochrome cd1-nitrite reductase, C-terminal domain superfamily / Cytochrome D1 heme domain / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / 8 Propeller / Methanol Dehydrogenase; Chain A / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / HEME D / HEME C / Nitrite reductase / Nitrite reductase
Similarity search - Component
Biological speciesPARACOCCUS PANTOTROPHUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSjogren, T. / Hajdu, J.
Citation
Journal: J.Biol.Chem. / Year: 2001
Title: The Structure of an Alternative Form of Paracoccus Pantotrophus Cytochrome Cd1 Nitrite Reductase
Authors: Sjogren, T. / Hajdu, J.
#1: Journal: Nature / Year: 1997
Title: Haem Ligand-Switching During Catalysis in Crystals of a Nitrogen Cycle Enzyme
Authors: Williams, P.A. / Fulop, V. / Garman, E.F. / Saunders, N.F.W. / Ferguson, S.J. / Hajdu, J.
#2: Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: The Anatomy of a Bifunctional Enzyme: Structural Basis for Reduction of Oxygen to Water and Synthesis of Nitric Oxide by Cytochrome Cd1
Authors: Fulop, V. / Moir, J.W.B. / Saunders, N.F.W. / Ferguson, S.J. / Hajdu, J.
History
DepositionMar 23, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2001Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_validate_chiral / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 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 CD1 NITRITE REDUCTASE
B: CYTOCHROME CD1 NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,09511
Polymers125,0932
Non-polymers3,0029
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)127.573, 127.573, 263.201
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CYTOCHROME CD1 NITRITE REDUCTASE


Mass: 62546.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ORGANISM FORMERLY KNOWN AS THIOSPHAERA PANTOTROPHA / Source: (natural) PARACOCCUS PANTOTROPHUS (bacteria) / Cellular location: PERIPLASM / References: UniProt: Q9FCQ0, UniProt: P72181*PLUS

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Non-polymers , 5 types, 251 molecules

#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Chemical ChemComp-DHE / HEME D


Mass: 712.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O10
#4: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#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.: 242 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsRESIDUES 1-47 OF CHAIN A ARE DISORDERED AND COULD NOT BE MODELLED RESIDUES 1-48 OF CHAIN B ARE DISORDERED.

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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: 4.3 Å3/Da / Density % sol: 71.16 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9
Details: HANGING DROP USING 2.1 M AMMONIUM SULPHATE AND 100 MM CHES PH 7.0 1 MM ASCORMBATE AND 2.5 UM PMS FROM REDUCTION OF PROTEIN WAS ALSO PRESENT IN CRYSTALLISATION.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-20 mg/mlprotein1drop
22 mMascorbate1drop
30.005 mMphenazine methosulphate1drop
42.0 Mammonium sulfate1reservoir
5100 mMCHES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.0232
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 5, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0232 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 83427 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 43.6 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 16.4
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.287 / % possible all: 93
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 93 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H9X

1h9x


Resolution: 2.4→20 Å / SU B: 6.61 / SU ML: 0.155 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.259 / ESU R Free: 0.219
Details: IN SUBUNIT A RESIDUES A 1 - A 47 ARE DISORDERED STRUCTURE AND WERE NOT MODELLED. IN SUBUNIT B RESIDUES B 1 - B 48 ARE DISORDERED STRUCTURE AND WERE NOT MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.269 -5 %RANDOM
Rwork0.238 ---
obs-83427 99.7 %-
Displacement parametersBiso mean: 40.2 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8107 0 202 242 8551
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.080.02
X-RAY DIFFRACTIONp_angle_d0.0260.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0240.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0047
X-RAY DIFFRACTIONp_chiral_restr0.980.15
X-RAY DIFFRACTIONp_singtor_nbd0.1840.3
X-RAY DIFFRACTIONp_multtor_nbd0.2430.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.160.3
X-RAY DIFFRACTIONp_planar_tor37
X-RAY DIFFRACTIONp_staggered_tor14.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.620
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.1

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