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- PDB-1aoq: CYTOCHROME CD1 NITRITE REDUCTASE WITH SUBSTRATE AND PRODUCT BOUND -

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Basic information

Entry
Database: PDB / ID: 1aoq
TitleCYTOCHROME CD1 NITRITE REDUCTASE WITH SUBSTRATE AND PRODUCT BOUND
ComponentsNITRITE REDUCTASE
KeywordsOXIDOREDUCTASE / ENZYME / NITRITE REDUCTASE
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
NITROGEN DIOXIDE / HEME D / PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / Nitrite reductase
Similarity search - Component
Biological speciesParacoccus pantotrophus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å
AuthorsWilliams, P.A. / Fulop, V.
CitationJournal: 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. / Ferguson, S.J. / Hajdu, J.
History
DepositionJul 9, 1997-
Revision 1.0Feb 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)127,9458
Polymers125,2112
Non-polymers2,7346
Water19,9611108
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7880 Å2
ΔGint-84 kcal/mol
Surface area37020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.700, 60.600, 100.100
Angle α, β, γ (deg.)90.00, 112.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.71811, 0.540276, 0.438658), (0.547106, -0.827834, 0.12396), (0.430108, 0.150976, -0.890064)
Vector: -29.30421, 5.38927, 106.88339)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NITRITE REDUCTASE /


Mass: 62605.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Paracoccus pantotrophus (bacteria) / Cellular location: PERIPLASM / References: UniProt: P72181

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Non-polymers , 5 types, 1114 molecules

#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-DHE / HEME D / Heme


Mass: 712.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O10
#4: Chemical ChemComp-2NO / NITROGEN DIOXIDE / Nitrogen dioxide


Mass: 46.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO2
#5: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1108 / 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: 2.39 Å3/Da / Density % sol: 48.54 %
Crystal growpH: 7
Details: 2.3 M AMMONIUM SULFATE 50MM POTASSIUM PHOSPHATE PH 7.0 CRYSTALS WERE REDUCED USING 16MM SODIUM DITHIONITE. CRYSTAL 2 SOAKED IN NITRITE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.88
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 101329 / % possible obs: 94.4 % / Observed criterion σ(I): 0 / Rsym value: 0.029
Reflection shellResolution: 1.8→1.86 Å / Rsym value: 0.072 / % possible all: 88.8
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 303438 / Rmerge(I) obs: 0.029

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementResolution: 1.8→30 Å / Rfactor Rfree error: 0.0031 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.197 4081 4 %RANDOM
Rwork0.176 ---
obs0.176 101286 94 %-
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8641 0 189 1108 9938
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2202 105 4 %
Rwork0.1785 2463 -
obs--90 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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