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- PDB-1ecd: STRUCTURE OF ERYTHROCRUORIN IN DIFFERENT LIGAND STATES REFINED AT... -

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Basic information

Entry
Database: PDB / ID: 1ecd
TitleSTRUCTURE OF ERYTHROCRUORIN IN DIFFERENT LIGAND STATES REFINED AT 1.4 ANGSTROMS RESOLUTION
ComponentsERYTHROCRUORIN (AQUO MET)
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / heme binding / extracellular region / metal ion binding
Similarity search - Function
Erythrocruorin / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Globin CTT-III
Similarity search - Component
Biological speciesChironomus thummi thummi (insect)
MethodX-RAY DIFFRACTION / Resolution: 1.4 Å
AuthorsSteigemann, W. / Weber, E.
Citation
Journal: J.Mol.Biol. / Year: 1979
Title: Structure of erythrocruorin in different ligand states refined at 1.4 A resolution.
Authors: Steigemann, W. / Weber, E.
#1: Journal: J.Mol.Biol. / Year: 1978
Title: The Structure of Oxy-Erythrocruorin at 1.4 Angstroms Resolution
Authors: Weber, E. / Steigemann, W. / Jones, T.A. / Huber, R.
#2: Journal: Eur.J.Biochem. / Year: 1971
Title: The Atomic Structure of Erythrocruorin in the Light of the Chemical Sequence and its Comparison with Myoglobin
Authors: Huber, R. / Epp, O. / Steigemann, W. / Formanek, H.
#3: Journal: J.Mol.Biol. / Year: 1970
Title: Structures of Deoxy-and Carbomonoxy-Erythrocruorin
Authors: Huber, R. / Epp, O. / Formanek, H.
History
DepositionMar 7, 1979Processing site: BNL
Revision 1.0Jul 5, 1979Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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: ERYTHROCRUORIN (AQUO MET)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4172
Polymers14,8011
Non-polymers6161
Water1,71195
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.300, 54.300, 35.600
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Atom site foot note1: RESIDUE PRO 74 IS A CIS-PROLINE.
2: AN OCCUPANCY OF 0.0 DENOTES ATOMS THAT HAVE NOT BEEN LOCALIZED IN THE ELECTRON DENSITY.
3: THIS HALF OCCUPIED WATER MOLECULE IS THE *SIXTH* LIGAND IN THE REDUCED DEOXY FORM. IT IS LOCATED APPROXIMATELY AT THE SAME POSITION AS THE WATER OF THE AQUO MET FORM 3 ANGSTROMS APART FROM THE IRON.

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Components

#1: Protein ERYTHROCRUORIN (AQUO MET)


Mass: 14800.792 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chironomus thummi thummi (insect) / Species: Chironomus thummi / Strain: thummi / References: UniProt: P02229
#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.: 95 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 39.9 %
Crystal grow
*PLUS
Method: other
Details: Braun, V., (1968) Hoppe Seylers Z Physiol Chem., 349, 197.

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.45 Å / Num. all: 27170 / Num. obs: 20751 / Rmerge(I) obs: 0.065

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Processing

RefinementHighest resolution: 1.4 Å
Refinement stepCycle: LAST / Highest resolution: 1.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1048 0 44 94 1186
Refinement
*PLUS
Lowest resolution: 7.8 Å / Rfactor obs: 0.183 / Highest resolution: 1.45 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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