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- PDB-1jf3: Crystal Structure Of Component III Glycera Dibranchiata Monomeric... -

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Basic information

Entry
Database: PDB / ID: 1jf3
TitleCrystal Structure Of Component III Glycera Dibranchiata Monomeric Hemoglobin
Componentsmonomer hemoglobin component III
KeywordsOXYGEN STORAGE/TRANSPORT / Glycera / monomer hemoglobin / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
: / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Globin, major monomeric component
Similarity search - Component
Biological speciesGlycera dibranchiata (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsPark, H.J. / Yang, C. / Treff, N. / Satterlee, J.D. / Kang, C.H.
CitationJournal: Proteins / Year: 2002
Title: Crystal Structures of Unligated and CN-Ligated Glycera dibranchiata Monomer Ferric Hemoglobin Components III and IV
Authors: Park, H.J. / Yang, C. / Treff, N. / Satterlee, J.D. / Kang, C.
History
DepositionJun 20, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: monomer hemoglobin component III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5752
Polymers14,9581
Non-polymers6161
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.133, 32.792, 40.949
Angle α, β, γ (deg.)90.0, 109.330, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein monomer hemoglobin component III


Mass: 14958.023 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Glycera dibranchiata (invertebrata) / References: UniProt: P02216
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.59 Å3/Da / Density % sol: 52.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, sodium cacodylate, ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Method: vapor diffusion / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
215 %PEG80001reservoir
350 mMsodium cacodylate1reservoir
40.1 Mammonium sulfate1reservoirpH6.5

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Apr 5, 2001 / Details: mirror
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→10 Å / Num. all: 14452 / Num. obs: 11757 / % possible obs: 81.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.083
Reflection shellResolution: 1.4→30 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.045 / % possible all: 92
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. obs: 9985 / % possible obs: 87 % / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 35 % / Rmerge(I) obs: 0.045

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→10 Å / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1576 15.6 %RANDOM
Rwork0.189 ---
all-11083 --
obs-10121 --
Refinement stepCycle: LAST / Resolution: 1.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1049 0 43 81 1173
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_angle_d2.3
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 10 Å / Num. reflection obs: 10341 / % reflection Rfree: 5 % / Rfactor obs: 0.188 / Rfactor Rfree: 0.2245 / Rfactor Rwork: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.17
LS refinement shell
*PLUS
Rfactor Rfree: 0.281 / Rfactor Rwork: 0.241 / Rfactor obs: 0.241

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