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- PDB-1dw2: STRUCTURE OF THE NITRIC OXIDE COMPLEX OF REDUCED SHP, AN OXYGEN B... -

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Basic information

Entry
Database: PDB / ID: 1dw2
TitleSTRUCTURE OF THE NITRIC OXIDE COMPLEX OF REDUCED SHP, AN OXYGEN BINDING CYTOCHROME C
ComponentsCYTOCHROME C
KeywordsOXYGEN STORAGE/TRANSPORT / cytochrome c / nitric oxide / disulfide bridge / asparagine ligation / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Protein of unknown function DUF1924, Cytochrome c-type protein SHP-like / Domain of unknown function (DUF1924) / 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 Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRIC OXIDE / Cytochrome c-type protein SHP
Similarity search - Component
Biological speciesRhodobacter sphaeroides (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsLeys, D. / Backers, K. / Meyer, T.E. / Hagen, W.R. / Cusanovich, M.A. / Van Beeumen, J.J.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: Crystal structures of an oxygen-binding cytochrome c from Rhodobacter sphaeroides.
Authors: Leys, D. / Backers, K. / Meyer, T.E. / Hagen, W.R. / Cusanovich, M.A. / Van Beeumen, J.J.
History
DepositionJan 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYTOCHROME C
B: CYTOCHROME C
C: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6499
Polymers34,7093
Non-polymers1,9396
Water4,900272
1
A: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2163
Polymers11,5701
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2163
Polymers11,5701
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: CYTOCHROME C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2163
Polymers11,5701
Non-polymers6462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.345, 103.498, 113.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein CYTOCHROME C /


Mass: 11569.791 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Rhodobacter sphaeroides (bacteria) / References: UniProt: P81238
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide / Nitric oxide


Mass: 30.006 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / 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: 3.53 Å3/Da / Density % sol: 65.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulfate, crystals were anaerobically reduced and NO added by reaction of dithionite with nitrite, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13.1 Mammonium sulfate1reservoir
2100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.54
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Aug 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 168292 / Num. obs: 25342 / % possible obs: 89.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.64 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 13.6
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.3 / % possible all: 90.3
Reflection
*PLUS
Num. measured all: 168292
Reflection shell
*PLUS
% possible obs: 90.3 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMACrefinement
RefinementResolution: 2.2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1267 5 %random
Rwork0.167 ---
all-168292 --
obs-25342 --
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2398 0 137 272 2807
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.03
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg3.4
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_improper_angle_d
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scangle_it

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