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- PDB-1flp: STRUCTURE OF THE SULFIDE-REACTIVE HEMOGLOBIN FROM THE CLAM LUCINA... -

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Basic information

Entry
Database: PDB / ID: 1flp
TitleSTRUCTURE OF THE SULFIDE-REACTIVE HEMOGLOBIN FROM THE CLAM LUCINA PECTINATA: CRYSTALLOGRAPHIC ANALYSIS AT 1.5 ANGSTROMS RESOLUTION
ComponentsHEMOGLOBIN I (AQUO MET)
KeywordsOXYGEN TRANSPORT
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-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin-1
Similarity search - Component
Biological speciesLucina pectinata (invertebrata)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsRizzi, M. / Wittenberg, J.B. / Ascenzi, P. / Fasano, M. / Coda, A. / Bolognesi, M.
Citation
Journal: J.Mol.Biol. / Year: 1994
Title: Structure of the sulfide-reactive hemoglobin from the clam Lucina pectinata. Crystallographic analysis at 1.5 A resolution.
Authors: Rizzi, M. / Wittenberg, J.B. / Coda, A. / Fasano, M. / Ascenzi, P. / Bolognesi, M.
#1: Journal: J.Mol.Biol. / Year: 1991
Title: Crystallization and Preliminary Data for the Ferric Form of Lucina Pectinata Hemoglobin I
Authors: Casale, E. / Lionetti, C. / Coda, A. / Merli, A. / Ascenzi, P. / Wittenberg, J.B. / Bolognesi, M.
#2: Journal: J.Biol.Chem. / Year: 1990
Title: Hemoglobins of the Lucina Pectinata(Slash)Bacteria Symbiosis. I. Molecular Properties, Kinetics and Equilibria of Reactions with Ligands
Authors: Kraus, D.W. / Wittenberg, J.B.
History
DepositionMay 16, 1994Processing site: BNL
Revision 1.0Jul 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMOGLOBIN I (AQUO MET)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,3762
Polymers14,7591
Non-polymers6161
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.970, 38.390, 42.650
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: THE C-TERMINAL STRETCH 136 - 142 HAS NOT BEEN YET CONFIRMED BY CHEMICAL ANALYSIS.

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Components

#1: Protein HEMOGLOBIN I (AQUO MET)


Mass: 14759.440 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lucina pectinata (invertebrata) / References: UniProt: P41260
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE HAS NOT BEEN REPORTED. IT WAS DETERMINED BY D. WALTZ AND S. VINOGRADOV.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.1 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 4.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
20.05 Macetate1drop
31.3 Mammonium sulfate1drop
42.6 Mammonium sulfate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. obs: 17354 / % possible obs: 90 % / Rmerge(I) obs: 0.061

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Processing

Software
NameClassification
ARP/wARPmodel building
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.5→15 Å / σ(F): 0 /
RfactorNum. reflection
obs0.17 17354
Refinement stepCycle: LAST / Resolution: 1.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 43 131 1212
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.02
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_deg2.7
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 all: 17354 / Rfactor all: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_angle_d2.7
X-RAY DIFFRACTIONo_plane_restr0.02

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