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- PDB-1hlm: AMINO ACID SEQUENCE OF A GLOBIN FROM THE SEA CUCUMBER CAUDINA (MO... -

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Basic information

Entry
Database: PDB / ID: 1hlm
TitleAMINO ACID SEQUENCE OF A GLOBIN FROM THE SEA CUCUMBER CAUDINA (MOLPADIA) ARENICOLA
ComponentsHEMOGLOBIN (CYANO MET)
KeywordsOXYGEN TRANSPORT
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-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Globin D, coelomic
Similarity search - Component
Biological speciesCaudina arenicola (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsHackert, M.L. / Mitchell, D.T. / Ernst, S.R.
Citation
Journal: Biochim.Biophys.Acta / Year: 1991
Title: Amino acid sequence of a globin from the sea cucumber Caudina (Molpadia) arenicola.
Authors: Mauri, F. / Omnaas, J. / Davidson, L. / Whitfill, C. / Kitto, G.B.
#1: 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.
#2: 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
DepositionAug 26, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 1.4Oct 9, 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_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: HEMOGLOBIN (CYANO MET)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3703
Polymers17,7271
Non-polymers6432
Water905
1
A: HEMOGLOBIN (CYANO MET)
hetero molecules

A: HEMOGLOBIN (CYANO MET)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7406
Polymers35,4552
Non-polymers1,2854
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)77.000, 77.000, 61.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HEMOGLOBIN (CYANO MET)


Mass: 17727.334 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caudina arenicola (invertebrata) / References: UniProt: P80017
#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.: 5 / 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: 2.57 Å3/Da / Density % sol: 52.15 %

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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: 2.9→5 Å / Rfactor Rwork: 0.19 / Rfactor obs: 0.19 / σ(F): 3
Refinement stepCycle: LAST / Resolution: 2.9→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1247 0 45 5 1297
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
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_deg3.51
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_d1.93
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

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