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- PDB-1fgj: X-RAY STRUCTURE OF HYDROXYLAMINE OXIDOREDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1fgj
TitleX-RAY STRUCTURE OF HYDROXYLAMINE OXIDOREDUCTASE
ComponentsHYDROXYLAMINE OXIDOREDUCTASE
KeywordsOXIDOREDUCTASE / NITRIFICATION
Function / homology
Function and homology information


hydroxylamine dehydrogenase / hydroxylamine oxidase activity / hydroxylamine oxidase / anaerobic respiration, using ammonium as electron donor / hydroxylamine oxidoreductase activity / anammoxosome / protein homotrimerization / oxidoreductase activity / heme binding / identical protein binding / metal ion binding
Similarity search - Function
Hydroxylamine Oxidoreductase; Chain A, domain 1 / Hydroxylamine Oxidoreductase; Chain A, domain 1 / Hydroxylamine Oxidoreductase; Chain A, domain 2 / Hydroxylamine Oxidoreductase; Chain A, domain 2 / Hydroxylamine oxidase / Seven times multi-haem cytochrome CxxCH / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / PROTOPORPHYRIN IX CONTAINING FE / Hydroxylamine oxidoreductase
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å
AuthorsTanaka, N. / Igarashi, N. / Moriyama, H.
CitationJournal: Nat.Struct.Biol. / Year: 1997
Title: The 2.8 A structure of hydroxylamine oxidoreductase from a nitrifying chemoautotrophic bacterium, Nitrosomonas europaea.
Authors: Igarashi, N. / Moriyama, H. / Fujiwara, T. / Fukumori, Y. / Tanaka, N.
History
DepositionMar 3, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HYDROXYLAMINE OXIDOREDUCTASE
B: HYDROXYLAMINE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,34118
Polymers123,4732
Non-polymers9,86816
Water0
1
A: HYDROXYLAMINE OXIDOREDUCTASE
hetero molecules

A: HYDROXYLAMINE OXIDOREDUCTASE
hetero molecules

A: HYDROXYLAMINE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,01127
Polymers185,2093
Non-polymers14,80224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area45340 Å2
ΔGint-675 kcal/mol
Surface area49290 Å2
MethodPISA, PQS
2
B: HYDROXYLAMINE OXIDOREDUCTASE
hetero molecules

B: HYDROXYLAMINE OXIDOREDUCTASE
hetero molecules

B: HYDROXYLAMINE OXIDOREDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,01127
Polymers185,2093
Non-polymers14,80224
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area45580 Å2
ΔGint-662 kcal/mol
Surface area49350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)96.200, 96.200, 265.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein HYDROXYLAMINE OXIDOREDUCTASE /


Mass: 61736.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Nitrosomonas europaea (bacteria) / References: UniProt: Q50925, hydroxylamine oxidase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 55 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
21.2 Mammonium sulfate1drop
325 mMTris-HCl1drop
42.4 Mammonium sulfate1reservoir
550 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorDetector: IMAGE PLATE / Date: May 6, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→40 Å / Num. obs: 33905 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Rmerge(I) obs: 0.79
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.166 / % possible all: 95
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameVersionClassification
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
CCP4data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→8 Å / σ(F): 2
Details: THE AUTHORS REFINED THE STRUCTURE BY ELIMINATING THE REPULSIVE FORCES BETWEEN HEME P460 AND ADJACENT TYR 467, BECAUSE AT PRESENT, X-PLOR CANNOT CONSTRAIN THE LINKAGE BETWEEN CRYSTALLOGRAPHIC ...Details: THE AUTHORS REFINED THE STRUCTURE BY ELIMINATING THE REPULSIVE FORCES BETWEEN HEME P460 AND ADJACENT TYR 467, BECAUSE AT PRESENT, X-PLOR CANNOT CONSTRAIN THE LINKAGE BETWEEN CRYSTALLOGRAPHIC RELATED SUBUNITS. THIS UNUSUAL LINKAGE IS THOUGHT TO BE COVALENT BOND.
RfactorNum. reflection% reflection
Rfree0.309 -5 %
Rwork0.23 --
obs0.23 33139 99.2 %
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7960 0 688 0 8648
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.23 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg1.629

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