[English] 日本語
Yorodumi
- PDB-1flp: STRUCTURE OF THE SULFIDE-REACTIVE HEMOGLOBIN FROM THE CLAM LUCINA... -

+
Open data


ID or keywords:

Loading...

-
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 domain profile. / Globin-like / Globin / Globin / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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.

-
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 / Heme B


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
Data collection

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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more