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- PDB-1hbi: CRYSTAL STRUCTURE OF OXYGENATED SCAPHARCA DIMERIC HEMOGLOBIN AT 1... -

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Basic information

Entry
Database: PDB / ID: 1hbi
TitleCRYSTAL STRUCTURE OF OXYGENATED SCAPHARCA DIMERIC HEMOGLOBIN AT 1.7 ANGSTROMS RESOLUTION
ComponentsHEMOGLOBIN (OXY)
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding / identical protein binding / cytoplasm
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
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Globin-1
Similarity search - Component
Biological speciesScapharca inaequivalvis (ark clam)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsRoyer Junior, W.E. / Condon, P.J.
Citation
Journal: J.Biol.Chem. / Year: 1994
Title: Crystal structure of oxygenated Scapharca dimeric hemoglobin at 1.7-A resolution.
Authors: Condon, P.J. / Royer Jr., W.E.
#1: Journal: J.Mol.Biol. / Year: 1994
Title: High-Resolution Crystallographic Analysis of a Co-Operative Dimeric Hemoglobin
Authors: Royer Junior, W.E.
#2: Journal: Science / Year: 1990
Title: Structural Transitions Upon Ligand Binding in a Cooperative Dimeric Hemoglobin
Authors: Royer Junior, W.E. / Hendrickson, W.A. / Chiancone, E.
History
DepositionJun 22, 1994Processing site: BNL
Revision 1.0Oct 15, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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: HEMOGLOBIN (OXY)
B: HEMOGLOBIN (OXY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2306
Polymers31,9332
Non-polymers1,2974
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-49 kcal/mol
Surface area12250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.200, 44.000, 83.500
Angle α, β, γ (deg.)90.00, 122.00, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.336, -0.2626, -0.9045), (-0.2626, -0.8961, 0.3577), (-0.9045, 0.3577, 0.2321)
Vector: 60.9, 2.78, 43.89)

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Components

#1: Protein HEMOGLOBIN (OXY)


Mass: 15966.319 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Scapharca inaequivalvis (ark clam) / Tissue: BLOOD / Organ: BLOOD / References: UniProt: P02213
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.27 Å3/Da / Density % sol: 45.89 %
Crystal
*PLUS
Density % sol: 44.7 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-20 mg/mlhemoglobin11
22.1-2.3 Mphosphate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 27434 / % possible obs: 86.5 % / Observed criterion σ(I): 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Rmerge(I) obs: 0.08

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.7→10 Å / σ(F): 4 /
RfactorNum. reflection% reflection
obs0.157 23385 73.7 %
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2248 0 90 218 2556
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.02
X-RAY DIFFRACTIONp_angle_d0.0330.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0460.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8441
X-RAY DIFFRACTIONp_mcangle_it1.2481.5
X-RAY DIFFRACTIONp_scbond_it1.8171.5
X-RAY DIFFRACTIONp_scangle_it2.7662
X-RAY DIFFRACTIONp_plane_restr0.010.02
X-RAY DIFFRACTIONp_chiral_restr0.1410.15
X-RAY DIFFRACTIONp_singtor_nbd0.170.5
X-RAY DIFFRACTIONp_multtor_nbd0.1770.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1880.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.93
X-RAY DIFFRACTIONp_staggered_tor1615
X-RAY DIFFRACTIONp_orthonormal_tor27.720
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ/X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS

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