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- PDB-1e2r: CYTOCHROME CD1 NITRITE REDUCTASE, REDUCED AND CYANIDE BOUND -

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Basic information

Entry
Database: PDB / ID: 1e2r
TitleCYTOCHROME CD1 NITRITE REDUCTASE, REDUCED AND CYANIDE BOUND
ComponentsNITRITE REDUCTASE
KeywordsOXIDOREDUCTASE / DENITRIFICATION / ELECTRON TRANSPORT / PERIPLASMIC / CYANIDE
Function / homology
Function and homology information


hydroxylamine reductase / hydroxylamine reductase activity / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / electron transfer activity / periplasmic space / 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
Similarity search - Component
Biological speciesPARACOCCUS DENITRIFICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsFulop, V.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: X-Ray Crystallographic Study of Cyanide Binding Provides Insights Into the Structure-Function Relationship for Cytochrome Cd1 Nitrite Reductase from Paracoccus Pantotrophus.
Authors: Jafferji, A. / Allen, J.W. / Ferguson, S.J. / Fulop, V.
#1: Journal: J.Mol.Biol. / Year: 1997
Title: Cytochrome Cd1 Structure: Unusual Haem Environments in a Nitrite Reductase and Analysis of Factors Contributing to Beta-Propeller Folds
Authors: Baker, S.C. / Saunders, N.F.W. / Willis, A.C. / Ferguson, S.J. / Hajdu, J. / Fulop, V.
#2: 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.
#3: Journal: Cell(Cambridge,Mass.) / Year: 1995
Title: The Anatomy of a Bifunctional Enzyme: Structural Basis for Reduction of Oxygen to Water and Synthesys of Nitric Oxide by Cytochrome Cd1
Authors: Fulop, V. / Moir, J.W.B. / Ferguson, S.J. / Hajdu, J.
History
DepositionMay 24, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 6, 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_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 / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)128,10510
Polymers125,2072
Non-polymers2,8988
Water24,1941343
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-89 kcal/mol
Surface area37220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.500, 60.900, 100.100
Angle α, β, γ (deg.)90.00, 111.90, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.721099, 0.545573, 0.427044), (0.538488, -0.829169, 0.150029), (0.435943, 0.121773, -0.891698)
Vector: -28.0723, 4.057, 107.0884)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NITRITE REDUCTASE / / CYTOCHROME CD1 / CYTOCHROME OXIDASE / HYDROXYLAMINE REDUCTASE / CYTOCHROME CD1 NITRITE REDUCTASE


Mass: 62603.633 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Details: SUBSP. PARACOCCUS PANTOTROPHUS FORMALLY KNOWN AS THIOSPHAERA PANTOTROPHA
Source: (natural) PARACOCCUS DENITRIFICANS (bacteria) / Cellular location: PERIPLASM
References: UniProt: P72181, nitrite reductase (NO-forming), hydroxylamine reductase

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Non-polymers , 5 types, 1351 molecules

#2: Chemical ChemComp-HEC / HEME C / Heme C


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


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


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1343 / 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: 2.41 Å3/Da / Density % sol: 40 %
Crystal growpH: 7
Details: 2.3 M AMMONIUM SULFATE, 50MM POTASSIUM PHOSPHATE, PH 7.0, AND CRYOPROTECTANT 15% GLYCEROL
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140 mg/mlprotein1drop
22.2-2.3 Mammonium sulfate1reservoir
350 mMpotassium phosphate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.83
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 15, 1998 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.83 Å / Relative weight: 1
ReflectionResolution: 1.59→25 Å / Num. obs: 156509 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 16.6 Å2 / Rsym value: 0.081 / Net I/σ(I): 16.8
Reflection shellResolution: 1.59→1.65 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 5.2 / Rsym value: 0.145 / % possible all: 96.7
Reflection
*PLUS
Num. measured all: 599187 / Rmerge(I) obs: 0.081

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
X-PLORphasing
Ophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AOF

1aof


Resolution: 1.59→25 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.208 6273 4 %RANDOM
Rwork0.192 ---
obs0.192 156509 97.8 %-
Displacement parametersBiso mean: 16.1 Å2
Refine analyzeLuzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.59→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8357 0 200 1343 9900
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.3
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.59→1.62 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 301 4 %
Rwork0.188 7201 -
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.3
LS refinement shell
*PLUS
Rfactor Rfree: 0.23

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