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

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Basic information

Entry
Database: PDB / ID: 1ecn
TitleSTRUCTURE OF ERYTHROCRUORIN IN DIFFERENT LIGAND STATES REFINED AT 1.4 ANGSTROMS RESOLUTION
ComponentsERYTHROCRUORIN (CYANO 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
CYANIDE ION / 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

Downloads & links

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Assembly

Deposited unit
A: ERYTHROCRUORIN (CYANO MET)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4433
Polymers14,8011
Non-polymers6432
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: IN THE CYANO MET STRUCTURE TWO ALTERNATE LOCATIONS HAVE BEEN FOUND FOR THE CATALYTIC RESIDUES HIS 58 AND ILE 62. THE PRESENCE OF THIS HALF OCCUPIED WATER MOLECULE THAT IS BOUND TO THE CN-LIGAND ...3: IN THE CYANO MET STRUCTURE TWO ALTERNATE LOCATIONS HAVE BEEN FOUND FOR THE CATALYTIC RESIDUES HIS 58 AND ILE 62. THE PRESENCE OF THIS HALF OCCUPIED WATER MOLECULE THAT IS BOUND TO THE CN-LIGAND CORRESPONDS TO THE USUAL CONFORMATION WHERE THE HISTIDINE POINTS OUT TO THE SOLVENT.

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Components

#1: Protein ERYTHROCRUORIN (CYANO 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-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: 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: 1.34 Å / Num. all: 46076 / Num. obs: 25946 / Rmerge(I) obs: 0.086

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Processing

RefinementHighest resolution: 1.4 Å
Refinement stepCycle: LAST / Highest resolution: 1.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1056 0 45 95 1196
Refinement
*PLUS
Lowest resolution: 7.8 Å / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS

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