[English] 日本語
Yorodumi
- PDB-1gli: DEOXYHEMOGLOBIN T38W (ALPHA CHAINS), V1G (ALPHA AND BETA CHAINS) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gli
TitleDEOXYHEMOGLOBIN T38W (ALPHA CHAINS), V1G (ALPHA AND BETA CHAINS)
Components(DEOXYHEMOGLOBIN) x 2
KeywordsOXYGEN TRANSPORT / MUTANT / ENGINEERED MUTANT / SITE DIRECTED MUTANT
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / inflammatory response / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / 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 / PHOSPHATE ION / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MUTANT-NATIVE DIFFERENCE MAP STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL / Resolution: 2.5 Å
AuthorsFermi, G. / Vallone, B.
CitationJournal: J.Biol.Chem. / Year: 1996
Title: Probing the alpha 1 beta 2 interface of human hemoglobin by mutagenesis. Role of the FG-C contact regions.
Authors: Vallone, B. / Bellelli, A. / Miele, A.E. / Brunori, M. / Fermi, G.
History
DepositionFeb 22, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Apr 18, 2018Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.process_site
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Feb 8, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other
Category: atom_site / atom_sites ...atom_site / atom_sites / database_PDB_matrix / pdbx_struct_conn_angle / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _atom_sites.fract_transf_vector[1] / _atom_sites.fract_transf_vector[2] / _atom_sites.fract_transf_vector[3] / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_struct_conn_angle.value / _pdbx_validate_planes.rmsd / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Mar 15, 2023Group: Advisory / Category: pdbx_database_remark
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DEOXYHEMOGLOBIN
B: DEOXYHEMOGLOBIN
C: DEOXYHEMOGLOBIN
D: DEOXYHEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,9409
Polymers62,3804
Non-polymers2,5615
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11750 Å2
ΔGint-107 kcal/mol
Surface area24070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.150, 83.590, 53.800
Angle α, β, γ (deg.)90.00, 99.34, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS TWO ALPHA AND TWO BETA CHAINS. ONLY ONE CHAIN OF EACH TYPE WAS DEPOSITED. THE COORDINATES FOR THE *C* AND *D* CHAINS WERE GENERATED FROM THE *A* AND *B* CHAINS, RESPECTIVELY, USING THE TRANSFORMATION (-X, Y, -Z).

-
Components

#1: Protein DEOXYHEMOGLOBIN


Mass: 15267.524 Da / Num. of mol.: 2 / Mutation: V1M, CHAIN A, C, T38W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P69905
#2: Protein DEOXYHEMOGLOBIN


Mass: 15922.265 Da / Num. of mol.: 2 / Mutation: V1M, CHAIN A, C, T38W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS STRUCTURE IS AN ENGINEERED POINT MUTANT OF HUMAN HEMOGLOBIN, T38AW OR THR 38 ALPHA (1 AND 2) -- ...THIS STRUCTURE IS AN ENGINEERED POINT MUTANT OF HUMAN HEMOGLOBIN, T38AW OR THR 38 ALPHA (1 AND 2) --> TRP. IT ALSO CONTAINS THE POINT MUTATIONS V1M, OR VAL 1 ALPHA (1 AND 2) --> MET AND VAL 1 BETA (1 AND 2) --> MET, WHICH ARE A CONSEQUENCE OF THE EXPRESSION SYSTEM USED. THE COORDINATE LIST IS IDENTICAL TO THE PDB ENTRY 3HHB EXCEPT FOR (1) THE SUBSTITUTION T38AW, (2) ADDITION OF WATER MOLECULE HOH 56 AND (3) APPROPRIATE CHANGES OF HEADER AND OTHER EXPLANATORY LINES. (4) EQUIVALENT ATOMS INTERCHANGED IN 22 RESIDUES TO CONFORM TO IUPAC/IUB SPECIFICATIONS (5) OCCUPANCY GIVEN AS FRACTION HERE VERSUS AS ELECTRON COUNT IN 3HHB

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 50 %
Crystal grow
*PLUS
pH: 6.5 / Method: unknown / Details: Perutz, M.F., (1968) J. Cryst. Growth, 2, 54.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 Mammonium sulfate11
22 M11(NH4)H2PO4
32 M11(NH4)2HPO4

-
Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Aug 10, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.48→22 Å / Num. obs: 15818 / % possible obs: 76.5 % / Redundancy: 2 % / Rmerge(I) obs: 0.096
Reflection
*PLUS
Num. obs: 15560 / Num. measured all: 25572

-
Processing

Software
NameClassification
MADNESdata reduction
CCP4data scaling
RefinementMethod to determine structure: MUTANT-NATIVE DIFFERENCE MAP STARTING MODEL FOR MOLECULAR REPLACEMENT: NULL
Highest resolution: 2.5 Å
Details: THE COORDINATES GIVEN HERE ARE IN THE ORTHOGONAL ANGSTROM SYSTEM STANDARD FOR HEMOGLOBINS. THE Y AXIS IS THE (NON-CRYSTALLOGRAPHIC) MOLECULAR DIAD AND THE X AXIS IS THE PSEUDO-DIAD WHICH ...Details: THE COORDINATES GIVEN HERE ARE IN THE ORTHOGONAL ANGSTROM SYSTEM STANDARD FOR HEMOGLOBINS. THE Y AXIS IS THE (NON-CRYSTALLOGRAPHIC) MOLECULAR DIAD AND THE X AXIS IS THE PSEUDO-DIAD WHICH RELATES THE ALPHA-1 AND BETA-1 CHAINS.
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 173 110 4685
Refinement
*PLUS
Num. reflection obs: 15442 / Rfactor obs: 0.135
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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