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- PDB-1hlb: Structural analysis of monomeric hemichrome and dimeric cyanomet ... -

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Basic information

Entry
Database: PDB / ID: 1hlb
TitleStructural analysis of monomeric hemichrome and dimeric cyanomet hemoglobins from Caudina arenicola
ComponentsHEMOGLOBIN (DEOXY)
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 C, coelomic
Similarity search - Component
Biological speciesCaudina arenicola (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsHackert, M.L. / Mitchell, D.T.
Citation
Journal: J.Mol.Biol. / Year: 1995
Title: Structural analysis of monomeric hemichrome and dimeric cyanomet hemoglobins from Caudina arenicola.
Authors: Mitchell, D.T. / Kitto, G.B. / Hackert, M.L.
#1: Journal: J.Protein Chem. / Year: 1992
Title: Amino Acid Sequence of the Coelomic C Globin from the Sea Cucumber Caudina (Molpadia) Arenicola
Authors: Mcdonald, G.D. / Davidson, L. / Kitto, G.B.
#2: Journal: J.Biol.Chem. / Year: 1979
Title: Preliminary Crystallographic Data on Monomeric and Dimeric Hemoglobins from the Sea Cucumber, Molpadia Arenicola
Authors: Carson, W.M. / Bowers, T.R. / Kitto, G.B. / Hackert, M.L.
#3: Journal: Biochim.Biophys.Acta / Year: 1976
Title: Functional Consequences of Ligand-Linked Dissociation in Hemoglobin from the Sea Cucumber Molpadia Arenicola
Authors: Bonaventura, C. / Bonaventura, J. / Kitto, B. / Brunori, M. / Antonini, E.
#4: Journal: COMP.BIOCHEM.PHYSIOL. B: BIOCHEM.MOL.BIOL. / Year: 1976
Title: N-Terminal Substitution of Some Sea Cucumber Hemoglobins
Authors: Kitto, G.B. / Erwin, D. / West, R. / Omnaas, J.
History
DepositionMar 22, 1994Processing site: BNL
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.pdbx_leaving_atom_flag / _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: HEMOGLOBIN (DEOXY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2012
Polymers17,5841
Non-polymers6161
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.740, 45.230, 40.920
Angle α, β, γ (deg.)90.00, 104.40, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: HEMICHROME COORDINATION OF HEME IRON ATOM WITH BOTH THE PROXIMAL AND DISTAL HISTIDINES COORDINATING TO THE HEME IRON ATOM.

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Components

#1: Protein HEMOGLOBIN (DEOXY)


Mass: 17584.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caudina arenicola (invertebrata) / References: UniProt: P80018
#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.: 111 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: unknown / Details: Carson, W.M., (1979) J.Biol.Chem., 254, 7400.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
17 mg/mlprotein11
24 %(w/v)PEG600011
310 mMphosphate11
41 mMEDTA11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.5→5 Å / σ(F): 3 /
RfactorNum. reflection
Rwork0.15 -
obs0.15 4916
Refinement stepCycle: LAST / Resolution: 2.5→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1236 0 43 111 1390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.59
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.15 / Rfactor Rwork: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 3.59

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