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- PDB-1ebt: HEMOGLOBIN I FROM THE CLAM LUCINA PECTINATA BOUND WITH CYANIDE -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1ebt
TitleHEMOGLOBIN I FROM THE CLAM LUCINA PECTINATA BOUND WITH CYANIDE
ComponentsHEMOGLOBIN
KeywordsOXYGEN TRANSPORT / HEMOGLOBIN / OXYGEN CARRIER / GLOBIN
Function / homology
Function and homology information


hemoglobin complex / oxygen transport / oxygen binding / heme binding / extracellular region / metal ion binding
Similarity search - Function
Erythrocruorin / Myoglobin-like, M family globin domain / 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 / Hemoglobin-1
Similarity search - Component
Biological speciesLucina pectinata (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsRosano, C. / Bolognesi, M. / Ascenzi, P.
CitationJournal: Biophys.J. / Year: 1999
Title: Cyanide binding to Lucina pectinata hemoglobin I and to sperm whale myoglobin: an x-ray crystallographic study.
Authors: Bolognesi, M. / Rosano, C. / Losso, R. / Borassi, A. / Rizzi, M. / Wittenberg, J.B. / Boffi, A. / Ascenzi, P.
History
DepositionNov 4, 1998Processing site: BNL
Revision 1.0Jan 13, 2000Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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.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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3873
Polymers14,7441
Non-polymers6432
Water1,42379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.670, 38.760, 42.530
Angle α, β, γ (deg.)90.00, 106.93, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HEMOGLOBIN


Mass: 14744.429 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Lucina pectinata (invertebrata) / References: UniProt: P41260
#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.: 79 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.8 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
pH: 5.75 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 %myoglobin11
2100 %ammonium sulfate11

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 1, 1995
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→24 Å / Num. obs: 12085 / % possible obs: 93 % / Redundancy: 2.2 %
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 24 Å / % possible obs: 93.3 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.054
Reflection shell
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 2 Å / Mean I/σ(I) obs: 5.1

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Processing

Software
NameVersionClassification
AMoREphasing
TNT5Erefinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FLP

1flp


Resolution: 1.9→24 Å / Isotropic thermal model: TNT BCORREL / σ(F): 0 / Stereochemistry target values: TNT PROTGEO /
Num. reflection% reflection
all12085 -
obs12085 93 %
Solvent computationBsol: 57.8 Å2 / ksol: 0.84 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1036 0 45 79 1160
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01511061.5
X-RAY DIFFRACTIONt_angle_deg2.39714862
X-RAY DIFFRACTIONt_dihedral_angle_d14.1766370
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.016282.5
X-RAY DIFFRACTIONt_gen_planes0.0111639
X-RAY DIFFRACTIONt_it2.321105910
X-RAY DIFFRACTIONt_nbd0.0621115
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.184
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_angle_deg2.4
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg14.1760
X-RAY DIFFRACTIONt_plane_restr0.0119

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