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- PDB-1yhu: Crystal structure of Riftia pachyptila C1 hemoglobin reveals nove... -

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Basic information

Entry
Database: PDB / ID: 1yhu
TitleCrystal structure of Riftia pachyptila C1 hemoglobin reveals novel assembly of 24 subunits.
Components
  • Giant hemoglobins B chain
  • hemoglobin A1 chain
  • hemoglobin B1a chain
  • hemoglobin B2 chain
KeywordsOXYGEN STORAGE/TRANSPORT / hemoglobin / globin fold / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / extracellular space / extracellular region
Similarity search - Function
Globin, extracellular / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Giant hemoglobins B chain / Hemoglobin B2 chain / Hemoglobin B1a chain / Hemoglobin A1 chain
Similarity search - Component
Biological speciesRiftia pachyptila (tube worm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Plus molecular averaging / Resolution: 3.15 Å
AuthorsFlores, J.F. / Fisher, C.R. / Carney, S.L. / Green, B.N. / Freytag, J.K. / Schaeffer, S.W. / Royer, W.E.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin.
Authors: Flores, J.F. / Fisher, C.R. / Carney, S.L. / Green, B.N. / Freytag, J.K. / Schaeffer, S.W. / Royer Jr, W.E.
History
DepositionJan 10, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 6, 2013Group: Data collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hemoglobin A1 chain
B: Giant hemoglobins B chain
C: hemoglobin B1a chain
D: hemoglobin B2 chain
E: hemoglobin A1 chain
F: Giant hemoglobins B chain
G: hemoglobin B1a chain
H: hemoglobin B2 chain
I: hemoglobin A1 chain
J: Giant hemoglobins B chain
K: hemoglobin B1a chain
L: hemoglobin B2 chain
M: hemoglobin A1 chain
N: Giant hemoglobins B chain
O: hemoglobin B1a chain
P: hemoglobin B2 chain
Q: hemoglobin A1 chain
R: Giant hemoglobins B chain
S: hemoglobin B1a chain
T: hemoglobin B2 chain
U: hemoglobin A1 chain
V: Giant hemoglobins B chain
W: hemoglobin B1a chain
X: hemoglobin B2 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)396,75484
Polymers380,40524
Non-polymers16,34960
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)195.840, 195.840, 308.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Details24mer assembled with D3 symmetry relating A1A2B1B2 tetramer. One entire assembly is present in the asymmetric unit.

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Components

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Protein , 4 types, 24 molecules AEIMQUBFJNRVCGKOSWDHLPTX

#1: Protein
hemoglobin A1 chain


Mass: 15795.024 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Riftia pachyptila (tube worm) / References: UniProt: Q8IFK4
#2: Protein
Giant hemoglobins B chain


Mass: 16158.232 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Riftia pachyptila (tube worm) / References: UniProt: P80592
#3: Protein
hemoglobin B1a chain


Mass: 15285.326 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Riftia pachyptila (tube worm) / References: UniProt: Q8IFK2
#4: Protein
hemoglobin B2 chain


Mass: 16162.318 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Riftia pachyptila (tube worm) / References: UniProt: Q8IFJ9

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Non-polymers , 3 types, 60 molecules

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


Mass: 616.487 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Chemical...
ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: O2
#7: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn

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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: 3.89 Å3/Da / Density % sol: 68.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6M ammonium sulfate, 0.1M HEPES, 0.1M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 3.15→50 Å / Num. all: 104444 / Num. obs: 104444 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.065 / Net I/σ(I): 11.3
Reflection shellResolution: 3.15→3.26 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.316 / % possible all: 99.9

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: Plus molecular averaging / Resolution: 3.15→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2707 5014 Random
Rwork0.2433 --
all0.2433 104444 -
obs0.2433 104444 -
Refinement stepCycle: LAST / Resolution: 3.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26712 0 1092 0 27804

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