[English] 日本語
Yorodumi
- PDB-2w72: DEOXYGENATED STRUCTURE OF A DISTAL SITE HEMOGLOBIN MUTANT PLUS XE -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2w72
TitleDEOXYGENATED STRUCTURE OF A DISTAL SITE HEMOGLOBIN MUTANT PLUS XE
Components(HUMAN HEMOGLOBIN ...) x 3
KeywordsOXYGEN TRANSPORT / IRON / HEME / GLYCATION / TRANSPORT / ACETYLATION / PHOSPHOPROTEIN / PACKING DEFECTS / DISEASE MUTATION / DISTAL SITE POINT MUTATION / HYDROPHOBIC CAVITIES / POLYMORPHISM / GLYCOPROTEIN / METAL-BINDING
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / 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 / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / response to hydrogen peroxide / 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 / 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 domain profile. / Globin-like / Globin / Globin ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / 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 / : / PHOSPHATE ION / XENON / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.07 Å
AuthorsMiele, A.E. / Draghi, F. / Sciara, G. / Johnson, K.A. / Renzi, F. / Vallone, B. / Brunori, M. / Savino, C.
CitationJournal: Biopolymers / Year: 2009
Title: Pattern of Cavities in Globins: The Case of Human Hemoglobin.
Authors: Savino, C. / Miele, A.E. / Draghi, F. / Johnson, K.A. / Sciara, G. / Brunori, M. / Vallone, B.
History
DepositionDec 19, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Mar 8, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HUMAN HEMOGLOBIN A
B: HUMAN HEMOGLOBIN A
C: HUMAN HEMOGLOBIN A
D: HUMAN HEMOGLOBIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,75335
Polymers62,3374
Non-polymers5,41631
Water14,664814
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17010 Å2
ΔGint-246 kcal/mol
Surface area22230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.957, 82.447, 53.531
Angle α, β, γ (deg.)90.00, 99.60, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
HUMAN HEMOGLOBIN ... , 3 types, 4 molecules ABDC

#1: Protein HUMAN HEMOGLOBIN A


Mass: 15190.353 Da / Num. of mol.: 1 / Fragment: CHAIN ALPHA, RESIDUES 2-142 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Cell: RED BLOOD CELL / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TB-1 / References: UniProt: P69905
#2: Protein HUMAN HEMOGLOBIN A


Mass: 15962.263 Da / Num. of mol.: 2 / Fragment: CHAIN BETA, RESIDUES 2-147 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Cell: RED BLOOD CELL / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TB-1 / References: UniProt: P68871
#3: Protein HUMAN HEMOGLOBIN A


Mass: 15222.417 Da / Num. of mol.: 1 / Fragment: CHAIN ALPHA, RESIDUES 2-142 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Cell: RED BLOOD CELL / Plasmid: PKK223-3 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TB-1 / References: UniProt: P69905

-
Non-polymers , 6 types, 845 molecules

#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Xe
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 814 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 30 TO TYR ENGINEERED RESIDUE IN CHAIN A, HIS 59 TO GLN ...ENGINEERED RESIDUE IN CHAIN A, LEU 30 TO TYR ENGINEERED RESIDUE IN CHAIN A, HIS 59 TO GLN ENGINEERED RESIDUE IN CHAIN B, LEU 29 TO TYR ENGINEERED RESIDUE IN CHAIN B, HIS 64 TO GLN ENGINEERED RESIDUE IN CHAIN C, LEU 30 TO TYR ENGINEERED RESIDUE IN CHAIN C, HIS 59 TO GLN ENGINEERED RESIDUE IN CHAIN D, LEU 29 TO TYR ENGINEERED RESIDUE IN CHAIN D, HIS 64 TO GLN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 32.5 % / Description: NONE
Crystal growpH: 6.5
Details: 3.2M AMMONIUM SULPHATE 0.1M AMMONIUM PHOSPHATE 0.3M K PHOSPHATE PH 6.7

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.8453
DetectorType: MARRESEARCH / Detector: CCD / Date: May 9, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8453 Å / Relative weight: 1
ReflectionResolution: 1.07→17.6 Å / Num. obs: 250223 / % possible obs: 91.1 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 8.54 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 25.8
Reflection shellResolution: 1.07→1.12 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 2.5 / % possible all: 90.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QI8

1qi8


Resolution: 1.07→17.32 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.802 / SU ML: 0.019 / Cross valid method: THROUGHOUT / ESU R: 0.029 / ESU R Free: 0.03 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.153 11023 5 %RANDOM
Rwork0.129 ---
obs0.13 208179 94.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.04 Å2
2--0.07 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.07→17.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4399 0 235 814 5448
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225760
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8992.0488096
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2065822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20224.348253
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.92715996
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6261516
X-RAY DIFFRACTIONr_chiral_restr0.1210.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024546
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2590.23219
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.320.23840
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2790.2710
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.3320.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3190.2115
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2540.283
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.87835766
X-RAY DIFFRACTIONr_sphericity_free10.0133840
X-RAY DIFFRACTIONr_sphericity_bonded6.63435451
LS refinement shellResolution: 1.07→1.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.176 744 -
Rwork0.151 14393 -
obs--88.68 %

+
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