[English] 日本語
Yorodumi
- PDB-5hbi: SCAPHARCA DIMERIC HEMOGLOBIN, MUTANT T72I, CO-LIGANDED FORM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hbi
TitleSCAPHARCA DIMERIC HEMOGLOBIN, MUTANT T72I, CO-LIGANDED FORM
ComponentsHEMOGLOBIN
KeywordsOXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / response to hypoxia / heme binding / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
: / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Globin-1
Similarity search - Component
Biological speciesScapharca inaequivalvis (ark clam)
MethodX-RAY DIFFRACTION / ISOMORPHOUS MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsRoyer Junior, W.E.
Citation
Journal: J.Mol.Biol. / Year: 1998
Title: Mutational destabilization of the critical interface water cluster in Scapharca dimeric hemoglobin: structural basis for altered allosteric activity.
Authors: Pardanani, A. / Gambacurta, A. / Ascoli, F. / Royer Jr., W.E.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1996
Title: Ordered Water Molecules as Key Allosteric Mediators in a Cooperative Dimeric Hemoglobin
Authors: Royer Junior, W.E. / Pardanani, A. / Gibson, Q.H. / Peterson, E.S. / Friedman, J.M.
#2: Journal: J.Mol.Biol. / Year: 1995
Title: A Single Mutation (Thr72-->Ile) at the Subunit Interface is Crucial for the Functional Properties of the Homodimeric Co-Operative Haemoglobin from Scapharca Inaequivalvis
Authors: Gambacurta, A. / Piro, M.C. / Coletta, M. / Clementi, M.E. / Polizio, F. / Desideri, A. / Santucci, R. / Ascoli, F.
#3: Journal: J.Mol.Biol. / Year: 1994
Title: High-Resolution Crystallographic Analysis of a Co-Operative Dimeric Hemoglobin
Authors: Royer Junior, W.E.
History
DepositionJun 24, 1998Processing site: BNL
Revision 1.0Nov 11, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _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
Revision 1.4Aug 9, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HEMOGLOBIN
B: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2486
Polymers31,9592
Non-polymers1,2894
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-56 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.270, 43.750, 83.350
Angle α, β, γ (deg.)90.00, 121.93, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.425781, -0.295485, -0.855219), (-0.154335, -0.907607, 0.390423), (-0.891567, 0.298225, 0.340838)
Vector: 63.10124, -2.55875, 40.27819)

-
Components

#1: Protein HEMOGLOBIN


Mass: 15979.356 Da / Num. of mol.: 2 / Mutation: T72I
Source method: isolated from a genetically manipulated source
Details: SCAPHARCA DIMERIC HEMOGLOBIN, HEME GROUP, PROTOPORPHYRIN IX IRON
Source: (gene. exp.) Scapharca inaequivalvis (ark clam) / Plasmid: PGAP1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM105 / 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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45 %
Crystal growpH: 7.5
Details: PROTEIN WAS CRYSTALLIZED FROM 2.3M NA/K PHOSPHATE AT PH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: batch method / Details: Royer Junior, W.E., (1994) J.Mol.Biol., 235, 657.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
140-50 mg/mlhemoglobin11
22.1-2.3 Mphosphate11

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Aug 1, 1996
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→20 Å / Num. obs: 33035 / % possible obs: 87.9 % / Observed criterion σ(I): 1 / Redundancy: 2.6 % / Rmerge(I) obs: 0.062
Reflection
*PLUS
Num. measured all: 85575 / Rmerge(I) obs: 0.0617

-
Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
RIGAKUdata reduction
RIGAKUdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: ISOMORPHOUS MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SDH

3sdh


Resolution: 1.6→10 Å / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.243 3318 10 %RANDOM
Rwork0.194 ---
obs0.194 29717 87 %-
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2234 0 90 193 2517
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d18.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.5
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
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg18.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.5

+
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