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- PDB-1ith: STRUCTURE DETERMINATION AND REFINEMENT OF HOMOTETRAMERIC HEMOGLOB... -

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Entry
Database: PDB / ID: 1ith
TitleSTRUCTURE DETERMINATION AND REFINEMENT OF HOMOTETRAMERIC HEMOGLOBIN FROM URECHIS CAUPO AT 2.5 ANGSTROMS RESOLUTION
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 / Hemoglobin F-I
Similarity search - Component
Biological speciesUrechis caupo (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsHackert, M. / Kolatkar, P. / Ernst, S.R. / Ogata, C.M. / Hendrickson, W.A. / Merritt, E.A. / Phizackerley, R.P.
Citation
Journal: Acta Crystallogr.,Sect.B / Year: 1992
Title: Structure determination and refinement of homotetrameric hemoglobin from Urechis caupo at 2.5 A resolution.
Authors: Kolatkar, P.R. / Ernst, S.R. / Hackert, M.L. / Ogata, C.M. / Hendrickson, W.A. / Merritt, E.A. / Phizackerley, R.P.
#1: Journal: J.Biol.Chem. / Year: 1988
Title: Novel Subunit Structure Observed for Noncooperative Hemoglobin from Urechis Caupo
Authors: Kolatkar, P.R. / Meador, W.E. / Stanfield, R.L. / Hackert, M.L.
History
DepositionDec 3, 1991Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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_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_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_asym_id / _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_asym_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 (CYANO MET)
B: HEMOGLOBIN (CYANO MET)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3826
Polymers30,0972
Non-polymers1,2854
Water2,702150
1
A: HEMOGLOBIN (CYANO MET)
B: HEMOGLOBIN (CYANO MET)
hetero molecules

A: HEMOGLOBIN (CYANO MET)
B: HEMOGLOBIN (CYANO MET)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,76312
Polymers60,1934
Non-polymers2,5708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)104.800, 54.900, 110.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.0027, -0.0007), (0.0004, -0.3737, 0.9276), (-0.0027, 0.9276, 0.3737)
Vector: 49.9616, 37.6654, -25.2898)
DetailsTHE TWO NON-CRYSTALLOGRAPHIC SUBUNITS ARE RELATED BY A MOLECULAR TWO-FOLD AXIS (179.8 DEGREE ROTATION) LOCATED IN THE BC PLANE AT 35 DEGREES FROM THE B AXIS (SEE REFERENCE 1). THE BACKBONE (N, C-ALPHA, C, O, + FE) RMS FIT = 0.317. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*.

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Components

#1: Protein HEMOGLOBIN (CYANO MET)


Mass: 15048.366 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Urechis caupo (invertebrata) / Gene: CDNA / References: UniProt: P06148
#2: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE 4 OF EACH CHAIN IS PRESENTED AS ALA IN THIS ENTRY. BOTH PIR AND SWISSPROT DATABASES LISTED ...RESIDUE 4 OF EACH CHAIN IS PRESENTED AS ALA IN THIS ENTRY. BOTH PIR AND SWISSPROT DATABASES LISTED THIS RESIDUE AS THR AT THE TIME THAT THIS ENTRY WAS PREPARED. THIS WAS BASED ON CDNA SEQUENCE OBTAINED FROM ONE CLONE. HOWEVER, AMINO ACID SEQUENCING OF THE GLOBINS SHOWED RESIDUE 4 TO BE ALA. THIS WAS CONFIRMED BY DIFFERENCE ELECTRON DENSITY MAPS.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.44 %
Crystal grow
*PLUS
pH: 7.8 / Method: unknown
Details: taken from Kolatkar, P.P. et al(1988), J. Biol. Chem., 263, 3462-3465.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mM11KCN
210 mMTris-HCl11
310 %PEG800011

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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
RefinementRfactor Rwork: 0.147 / Rfactor obs: 0.147 / Highest resolution: 2.5 Å
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2126 0 90 150 2366
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_deg3.33
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
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 5 Å / Num. reflection obs: 8350 / σ(I): 3 / Rfactor obs: 0.147
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3.33
X-RAY DIFFRACTIONx_dihedral_angle_d21.046
X-RAY DIFFRACTIONx_dihedral_angle_deg2.027

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