[English] 日本語
Yorodumi
- PDB-1a0u: HEMOGLOBIN (VAL BETA1 MET) MUTANT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a0u
TitleHEMOGLOBIN (VAL BETA1 MET) MUTANT
Components
  • HEMOGLOBIN (ALPHA CHAIN)
  • HEMOGLOBIN (BETA CHAIN)
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / 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 / Late endosomal microautophagy / Heme signaling / response to hydrogen peroxide / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / regulation of blood pressure / 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 / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / ISOMORPHOUS WITH DEOXYHEMOGLOBIN A / Resolution: 2.14 Å
AuthorsKavanaugh, J.S. / Arnone, A.
Citation
Journal: Biochemistry / Year: 1998
Title: High-resolution crystal structures of human hemoglobin with mutations at tryptophan 37beta: structural basis for a high-affinity T-state,.
Authors: Kavanaugh, J.S. / Weydert, J.A. / Rogers, P.H. / Arnone, A.
#1: Journal: Biochemistry / Year: 1992
Title: High-Resolution X-Ray Study of Deoxyhemoglobin Rothschild 37 Beta Trp-->Arg: A Mutation that Creates an Intersubunit Chloride-Binding Site
Authors: Kavanaugh, J.S. / Rogers, P.H. / Case, D.A. / Arnone, A.
History
DepositionDec 8, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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 (ALPHA CHAIN)
B: HEMOGLOBIN (BETA CHAIN)
C: HEMOGLOBIN (ALPHA CHAIN)
D: HEMOGLOBIN (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6118
Polymers62,1454
Non-polymers2,4664
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-104 kcal/mol
Surface area23240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.200, 99.300, 65.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.77003, 0.46993, -0.43153), (0.47066, -0.87504, -0.11306), (-0.43074, -0.11605, -0.89499)
Vector: -14.26744, 37.77566, -17.43522)

-
Components

#1: Protein HEMOGLOBIN (ALPHA CHAIN)


Mass: 15150.353 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: RED BLOOD CELL / Gene: HUMAN BETA GLOBIN / Organ: BLOOD / Gene (production host): HUMAN BETA GLOBIN / Production host: Escherichia coli (E. coli) / References: UniProt: P69905
#2: Protein HEMOGLOBIN (BETA CHAIN)


Mass: 15922.265 Da / Num. of mol.: 2 / Mutation: V1M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: RED BLOOD CELL / Gene: HUMAN BETA GLOBIN / Organ: BLOOD / Gene (production host): HUMAN BETA GLOBIN / Production host: Escherichia coli (E. coli) / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water / 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: 2.46 Å3/Da / Density % sol: 50 %
Description: PDB ENTRY 1HHB WAS USED AS THE STARTING MODEL FOR LEAST-SQUARES REFINEMENT.
Crystal growpH: 7
Details: 10.5% PEG 6000 10 MM POTASSIUM PHOSPHATE PH 7.0 100 MM POTASSIUM CHLORIDE 3 MM SODIUM DITHIONITE
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mMpotassium phosphate11
2100 mM11KCl
33 mMsodium dithionite11
410.0 %PEG600011
510 mg/mlhemoglobin11

-
Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Aug 1, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.14→25 Å / Num. obs: 35230 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 11.2
Reflection shellResolution: 2.14→2.3 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.173 / Mean I/σ(I) obs: 2.25 / Rsym value: 0.173 / % possible all: 91
Reflection
*PLUS
Num. measured all: 267646

-
Processing

Software
NameClassification
PROLSQrefinement
SDMSdata reduction
SDMSdata scaling
RefinementMethod to determine structure: ISOMORPHOUS WITH DEOXYHEMOGLOBIN A
Starting model: PDB ENTRY 1HHB

1hhb
PDB Unreleased entry


Resolution: 2.14→8 Å / Cross valid method: A POSTERIORI / σ(F): 2
Details: THE STARTING MODEL FOR REFINEMENT WAS PDB ENTRY 1HHB.
RfactorNum. reflection% reflectionSelection details
Rfree0.239 3082 10 %RANDOM
Rwork0.172 ---
obs0.179 33920 98 %-
Displacement parametersBiso mean: 24.8 Å2
Refinement stepCycle: LAST / Resolution: 2.14→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 172 193 4751
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.01
X-RAY DIFFRACTIONp_angle_d0.0240.015
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0380.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.22
X-RAY DIFFRACTIONp_mcangle_it3.13
X-RAY DIFFRACTIONp_scbond_it7.44
X-RAY DIFFRACTIONp_scangle_it10.46
X-RAY DIFFRACTIONp_plane_restr0.0110.01
X-RAY DIFFRACTIONp_chiral_restr0.1320.08
X-RAY DIFFRACTIONp_singtor_nbd0.1620.2
X-RAY DIFFRACTIONp_multtor_nbd0.1730.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1760.2
X-RAY DIFFRACTIONp_planar_tor2.35
X-RAY DIFFRACTIONp_staggered_tor19.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor31.725
X-RAY DIFFRACTIONp_special_tor

+
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