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- PDB-1hbg: GLYCERA DIBRANCHIATA HEMOGLOBIN. STRUCTURE AND REFINEMENT AT 1.5 ... -

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Basic information

Entry
Database: PDB / ID: 1hbg
TitleGLYCERA DIBRANCHIATA HEMOGLOBIN. STRUCTURE AND REFINEMENT AT 1.5 ANGSTROMS RESOLUTION
ComponentsHEMOGLOBIN (CARBONMONOXY)
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Globin, major monomeric component
Similarity search - Component
Biological speciesGlycera dibranchiata (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsArents, G.A. / Braden, B.C. / Padlan, E.A. / Love, W.E.
CitationJournal: J.Mol.Biol. / Year: 1989
Title: Glycera dibranchiata hemoglobin. Structure and refinement at 1.5 A resolution.
Authors: Arents, G. / Love, W.E.
History
DepositionFeb 11, 1991Processing site: BNL
Revision 1.0Jul 15, 1992Provider: 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 1.4Feb 7, 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 / struct_site
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 / _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 (CARBONMONOXY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,5803
Polymers14,9351
Non-polymers6442
Water2,792155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.750, 83.150, 38.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: SEVEN RESIDUES HAVE THEIR SIDE CHAINS MODELED IN MORE THAN ONE CONFORMATION. THEY ARE LEU 31, MET 79, LYS 84, ASN 95, SER 109, SER 112, AND SER 143. ALSO SEE REMARK 6 ABOVE.

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Components

#1: Protein HEMOGLOBIN (CARBONMONOXY)


Mass: 14935.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Glycera dibranchiata (invertebrata) / References: UniProt: P02216
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHERE ARE A NUMBER OF SEQUENCE DIFFERENCES BETWEEN THE SEQUENCE PRESENTED IN THIS ENTRY AND THAT IN ...THERE ARE A NUMBER OF SEQUENCE DIFFERENCES BETWEEN THE SEQUENCE PRESENTED IN THIS ENTRY AND THAT IN PROTEIN IDENTIFICATION RESOURCE (PIR) ENTRY GGNW1B WHICH IS BASED ON THE SEQUENCE OF T.IMAMURA,T.O.BALDWIN,A.RIGGS, J.BIOL.CHEM., V. 247, P. 2785 (1972). THE SUBSTITUTION OF ALA FOR ASP AT RESIDUE 20 AND PHE FOR HIS AT RESIDUE 34 AGREE WITH THE PARTIAL SEQUENCE OF S.L.LI,A.F.RIGGS, BIOCHIM.BIOPHYS.ACTA, V. 236, P. 208 (1971)). RESIDUE 29 IS ASP IN THE SEQUENCE OF IMAMURA ET AL. AND GLU IN THE SEQUENCE OF LI AND RIGGS. RESIDUE 29 HAS BEEN MODELED AS LYS IN THIS ENTRY DUE TO THE ABSENCE OF SIDE CHAIN BRANCHING IN THE ELECTRON DENSITY MAP. RESIDUE 54 WAS CHANGED FROM ALA TO GLY AND RESIDUE 100 WAS CHANGED FROM GLY TO ALA; THE CORRESPONDING NEGATIVE AND POSITIVE DIFFERENCE ELECTRON DENSITY PEAKS IMMEDIATELY DISAPPEARED. THE SUBSTITUTION OF ALA FOR ASP AT RESIDUE 57 AGREES WELL WITH THE X-RAY DATA BUT MAY NOT REPRESENT THE TRUTH. THE SIDE-CHAIN OF RESIDUE 57 IS COMPLETELY EXPOSED TO THE SOLVENT; THEREFORE IT IS POSSIBLE THAT THE CG AND OD ATOMS ARE PRESENT BUT EXIST IN TOO MANY CONFORMATIONS IN THE CRYSTAL FOR ANY CORRESPONDING ELECTRON DENSITY TO BE VISIBLE. NEVERTHELESS, ALA WAS SUBSTITUTED AT RESIDUE 57 BECAUSE THERE IS NO ELECTRON DENSITY TO WHICH THE ASPARTATE ATOMS COULD BE FITTED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.52 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6.8 / Method: unknown / Details: took Padlan & Love (1974) from original paper
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
13.2 M11NaCl
20.03 Mpotassium phosphate11
3hemoglobin11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 5 Å / Num. obs: 15951 / Observed criterion σ(I): 1.5 / Num. measured all: 39770

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.146 / Highest resolution: 1.5 Å
Details: LEUCINE 31 SHOWS EQUAL WEIGHT FOR EACH OF THE THREE POSSIBLE GAUCHE CONFORMATIONS OF ATOMS CD1 AND CD2. THESE ARE PRESENTED AS THREE ALTERNATE CONFORMATIONS WITH AN OCCUPANCY OF 0.33 EACH. ...Details: LEUCINE 31 SHOWS EQUAL WEIGHT FOR EACH OF THE THREE POSSIBLE GAUCHE CONFORMATIONS OF ATOMS CD1 AND CD2. THESE ARE PRESENTED AS THREE ALTERNATE CONFORMATIONS WITH AN OCCUPANCY OF 0.33 EACH. NOTE THAT ONLY THREE SETS OF COORDINATES WERE USED TO MODEL THIS DISORDER AND, THEREFORE, THE SIX ATOMS APPEAR AS THREE ATOMS IN A GRAPHICAL VIEW OF THE ENTRY.
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1062 0 45 155 1262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.027
X-RAY DIFFRACTIONp_angle_d0.038
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.012
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Rfactor obs: 0.146
Solvent computation
*PLUS
Displacement parameters
*PLUS

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