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- PDB-1gq1: CYTOCHROME CD1 NITRITE REDUCTASE, Y25S mutant, OXIDISED FORM -

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Basic information

Entry
Database: PDB / ID: 1gq1
TitleCYTOCHROME CD1 NITRITE REDUCTASE, Y25S mutant, OXIDISED FORM
ComponentsCYTOCHROME CD1 NITRITE REDUCTASE
KeywordsOXIDOREDUCTASE / REDUCTASE / ENZYME / NITRITE REDUCTASE / DENITRIFICATION / ELECTRON TRANSPORT / PERIPLASMIC
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
HEME D / HEME C / Nitrite reductase / Nitrite reductase
Similarity search - Component
Biological speciesPARACOCCUS PANTOTROPHUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSjogren, T. / Gordon, E.H.J. / Lofqvist, M. / Richter, C.D. / Hajdu, J. / Ferguson, S.J.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Structure and Kinetic Properties of Paracoccus Pantotrophus Cytochrome Cd1 Nitrite Reductase with the D1 Heme Active Site Ligand Tyrosine 25 Replaced by Serine
Authors: Gordon, E.H.J. / Sjogren, T. / Lofqvist, M. / Richter, C.D. / Allen, J. / Higham, C. / Hajdu, J. / Fulop, V. / Ferguson, S.J.
#1: 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. / Ferguson, S.J. / Hajdu, J.
History
DepositionNov 19, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 28, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 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_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_conn_type / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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.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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 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)128,64817
Polymers124,9412
Non-polymers3,70715
Water24,3921354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-211.5 kcal/mol
Surface area36840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.797, 60.600, 100.340
Angle α, β, γ (deg.)90.00, 112.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein CYTOCHROME CD1 NITRITE REDUCTASE


Mass: 62470.438 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PARACOCCUS PANTOTROPHUS (bacteria) / Plasmid: PEG276 / Production host: PARACOCCUS PANTOTROPHUS (bacteria) / Strain (production host): EG6202
References: UniProt: Q9FCQ0, UniProt: P72181*PLUS, EC: 1.9.3.2, nitrite reductase (NO-forming)

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Non-polymers , 5 types, 1369 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1354 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED MUTATION TYR 54 SER
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51 %
Crystal growpH: 7
Details: 2.3 M AMMONIUM SULFATE, 50MM POTASSIUM PHOSPHATE, PH 7.0, AND CRYOPROTECTANT 18% GLYCEROL
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion, hanging drop / Details: Fulop, V., (1993) J. Mol. Biol., 232, 1211.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
21.1-1.15 Mammonium sulfate1drop
325 mMpotassium phosphate1drop
42.2-2.3 Mammonium sulfate1reservoir
550 mMpotassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 6, 2000 / Details: MIRRORS
RadiationMonochromator: SI CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 233906 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.8
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 4.3 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 30 Å / % possible obs: 100 % / Num. measured all: 812906
Reflection shell
*PLUS
Highest resolution: 1.4 Å / % possible obs: 100 % / Mean I/σ(I) obs: 4.72

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QKS

1qks


Resolution: 1.4→30 Å / SU B: 0.79 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.05 / ESU R Free: 0.05
RfactorNum. reflection% reflectionSelection details
Rfree0.175 11695 5 %RANDOM
Rwork0.159 ---
obs-233906 100 %-
Displacement parametersBiso mean: 10.9 Å2
Refinement stepCycle: LAST / Resolution: 1.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8678 0 242 1354 10274
Refinement
*PLUS
Lowest resolution: 30 Å / % reflection Rfree: 4 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.4

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