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- PDB-2lhb: REFINEMENT OF A MOLECULAR MODEL FOR LAMPREY HEMOGLOBIN FROM PETRO... -

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Basic information

Entry
Database: PDB / ID: 2lhb
TitleREFINEMENT OF A MOLECULAR MODEL FOR LAMPREY HEMOGLOBIN FROM PETROMYZON MARINUS
ComponentsHEMOGLOBIN V (CYANO MET)
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / oxidoreductase activity / iron ion binding / heme binding
Similarity search - Function
Globin, lamprey/hagfish type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Globin-5
Similarity search - Component
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsHonzatko, R.B. / Hendrickson, W.A. / Love, W.E.
Citation
Journal: J.Mol.Biol. / Year: 1985
Title: Refinement of a molecular model for lamprey hemoglobin from Petromyzon marinus.
Authors: Honzatko, R.B. / Hendrickson, W.A. / Love, W.E.
#1: Journal: J.Mol.Biol. / Year: 1973
Title: Crystal Structure Analysis of Sea Lamprey Hemoglobin at 2 Angstroms Resolution
Authors: Hendrickson, W.A. / Love, W.E. / Karle, J.
#2: Journal: Nature New Biol. / Year: 1971
Title: Structure of Lamprey Haemoglobin
Authors: Hendrickson, W.A. / Love, W.E.
History
DepositionAug 16, 1985Processing site: BNL
SupersessionJan 21, 1986ID: 1LHB
Revision 1.0Jan 21, 1986Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / 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 1.4Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEMOGLOBIN V (CYANO MET)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,9343
Polymers16,2921
Non-polymers6432
Water3,873215
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.570, 96.620, 31.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: SEE REMARK 5. / 2: SEE REMARK 7.

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Components

#1: Protein HEMOGLOBIN V (CYANO MET)


Mass: 16291.678 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / References: UniProt: P02208
#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.: 215 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE TWO CHANGES IN THE SEQUENCE IN THIS ENTRY FROM THAT DETERMINED CHEMICALLY (S.L.LI, A. ...THERE ARE TWO CHANGES IN THE SEQUENCE IN THIS ENTRY FROM THAT DETERMINED CHEMICALLY (S.L.LI, A.RIGGS, J.BIOL.CHEM., V. 245, P. 6149 (1970)). LEU 98 AND ARG 99 WERE INSERTED AFTER LYS 97, WHILE MET 138 AND SER 139 HAVE REPLACED AN ARG.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130-35 mg/mlprotein1drop
210 mM1dropNaCN
32.1 Mpotassium phosphate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

RefinementRfactor Rwork: 0.142 / Highest resolution: 2 Å
Details: ELEVEN RESIDUES ARE PRESENTED WITH ALTERNATE CONFORMATIONS BASED ON DENSITY. LYS 18 HAS NO DENSITY BEYOND CB AND LYS 54 HAS NO DENSITY BEYOND CG. THE SIDE CHAINS OF THESE TWO RESIDUES WERE ...Details: ELEVEN RESIDUES ARE PRESENTED WITH ALTERNATE CONFORMATIONS BASED ON DENSITY. LYS 18 HAS NO DENSITY BEYOND CB AND LYS 54 HAS NO DENSITY BEYOND CG. THE SIDE CHAINS OF THESE TWO RESIDUES WERE MODELED USING REASONABLE STEREOCHEMICAL CRITERIA AND ARE PRESENTED WITH ALTERNATE CONFORMATIONS. SEE THE JRNL REFERENCE ABOVE FOR FURTHER DETAILS. IN ALL OF THESE RESIDUES HYDROGEN ATOMS ARE INCLUDED FOR ONE CONFORMATION ONLY. RESIDUE 29 HAS AN EQUAL MIX OF THR AND ASP ACCORDING TO SEQUENCE WORK. THIS RESIDUE IS PRESENTED BELOW WITH CONFORMATION A REPRESENTING THR AND CONFORMATION B REPRESENTING ASP. PLEASE NOTE, HOWEVER, THAT BOTH CONFORMATIONS HAVE BEEN ASSIGNED RESIDUE NAME THR ON THE ATOM AND SEQRES RECORDS BELOW.
Refinement stepCycle: LAST / Highest resolution: 2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1152 0 45 215 1412
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.014
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg1.5
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Num. reflection obs: 7979 / Highest resolution: 2 Å / Rfactor obs: 0.142
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_angle_d1.5
X-RAY DIFFRACTIONo_dihedral_angle_d0.048
X-RAY DIFFRACTIONo_plane_restr0.012
X-RAY DIFFRACTIONo_chiral_restr0.15
X-RAY DIFFRACTIONo_mcbond_it1.211.5
X-RAY DIFFRACTIONo_scbond_it2.1272
X-RAY DIFFRACTIONo_mcangle_it1.9032
X-RAY DIFFRACTIONo_scangle_it3.3283

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