[English] 日本語
Yorodumi
- PDB-1ch4: MODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA (F133V) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ch4
TitleMODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA (F133V)
ComponentsMODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA
KeywordsOXYGEN TRANSPORT / CHIMERA PROTEIN / RESPIRATORY PROTEIN / HEME
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 / inflammatory response / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / cytosol
Similarity search - Function
Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsShirai, T. / Fujikake, M. / Yamane, T. / Inaba, K. / Ishimori, K. / Morishima, I.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Crystal structure of a protein with an artificial exon-shuffling, module M4-substituted chimera hemoglobin beta alpha, at 2.5 A resolution.
Authors: Shirai, T. / Fujikake, M. / Yamane, T. / Inaba, K. / Ishimori, K. / Morishima, I.
#1: Journal: Proteins / Year: 1998
Title: Design, Construction, Crystallization, and Preliminary X-Ray Studies of a Fine-Tuning Mutant (F133V) of Module-Substituted Chimera Hemoglobin
Authors: Shirai, T. / Fujikake, M. / Yamane, T. / Inaba, K. / Ishimori, K. / Morishima, I.
History
DepositionJun 11, 1998Processing site: BNL
Revision 1.0Apr 27, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA
B: MODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA
C: MODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA
D: MODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,82712
Polymers63,2494
Non-polymers2,5788
Water75742
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12980 Å2
ΔGint-118 kcal/mol
Surface area22160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.870, 81.310, 55.110
Angle α, β, γ (deg.)90.00, 90.96, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.908143, -0.144029, -0.393105), (-0.137863, -0.783712, 0.605631), (-0.39531, 0.604194, 0.691867)
Vector: 36.64821, -4.80501, 10.26913)
DetailsTHE CRYSTALLOGRAPHIC ASYMMETRIC UNIT IS THE CHIMERA-TETRAMER.

-
Components

#1: Protein
MODULE-SUBSTITUTED CHIMERA HEMOGLOBIN BETA-ALPHA


Mass: 15812.229 Da / Num. of mol.: 4 / Mutation: F133V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P68871*PLUS
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-CMO / CARBON MONOXIDE


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


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Details: Shirai, T., (1998) Proteins: Struct.,Funct., Genet., 32, 263.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
125 %(w/v)PEG40001reservoir
20.1 Msodium potassium phosphate1reservoir
30.600 mMprotein1drop
450 mMsodium phosphate1drop

-
Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Oct 1, 1996 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 17766 / % possible obs: 91.2 % / Observed criterion σ(I): 1 / Redundancy: 4.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 5.6
Reflection shellResolution: 2.5→2.59 Å / % possible all: 82.5

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CN-HEMOGLOBIN H

Resolution: 2.5→8 Å / Cross valid method: THROUGHOUT / σ(F): 3
Details: THIS PROTEIN WAS CONSTRUCTED BY REPLACING MODULE M4, 97(FG4)-146(HC3), OF BETA-SUBUNIT OF HUMAN HEMOGLOBIN WITH THE CORRESPONDING REGION, 92(FG4)-141(HC3), OF THE ALPHA-SUBUNIT. A POINT ...Details: THIS PROTEIN WAS CONSTRUCTED BY REPLACING MODULE M4, 97(FG4)-146(HC3), OF BETA-SUBUNIT OF HUMAN HEMOGLOBIN WITH THE CORRESPONDING REGION, 92(FG4)-141(HC3), OF THE ALPHA-SUBUNIT. A POINT MUTATION F133V(H11) WAS INTRODUCED TO INCREASE THE STABILITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.244 787 5 %RANDAM
Rwork0.188 ---
obs0.188 15212 81.4 %-
Displacement parametersBiso mean: 27.9 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 7 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4528 0 180 42 4750
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg2.646
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d19.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.475
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
Refine LS restraints NCSNCS model details: STRICT
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg19.906
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.475

+
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