[English] 日本語
Yorodumi
- PDB-4mqk: Carbonmonoxy Structure of the Human Fetal Hemoglobin Mutant HbF T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mqk
TitleCarbonmonoxy Structure of the Human Fetal Hemoglobin Mutant HbF Toms River alphawtgammaV67M
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit gamma-2
KeywordsOXYGEN TRANSPORT / oxygen-transport / autooxidation
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process ...nitric oxide transport / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process / oxygen carrier activity / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / peroxidase activity / Factors involved in megakaryocyte development and platelet production / blood microparticle / iron ion binding / heme binding / 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 domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit gamma-2 / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.242 Å
AuthorsSoman, J. / Olson, J.S.
CitationJournal: TO BE PUBLISHED
Title: Carbonmonoxy Structure of the Human Fetal Hemoglobin Mutant HbF Toms River alphawtgammaV67M
Authors: Soman, J. / Olson, J.S.
History
DepositionSep 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Other
Revision 1.2Oct 8, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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_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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_ref_seq_dif.details / _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 subunit alpha
B: Hemoglobin subunit gamma-2
C: Hemoglobin subunit alpha
D: Hemoglobin subunit gamma-2
E: Hemoglobin subunit alpha
F: Hemoglobin subunit gamma-2
G: Hemoglobin subunit alpha
H: Hemoglobin subunit gamma-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,89922
Polymers124,7998
Non-polymers5,10014
Water5,116284
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit gamma-2
E: Hemoglobin subunit alpha
F: Hemoglobin subunit gamma-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,94911
Polymers62,3994
Non-polymers2,5507
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-30 kcal/mol
Surface area24940 Å2
MethodPISA
2
C: Hemoglobin subunit alpha
D: Hemoglobin subunit gamma-2
G: Hemoglobin subunit alpha
H: Hemoglobin subunit gamma-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,94911
Polymers62,3994
Non-polymers2,5507
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-34 kcal/mol
Surface area24730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.040, 52.229, 106.381
Angle α, β, γ (deg.)90.00, 114.27, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 4 / Mutation: V67M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P69905
#2: Protein
Hemoglobin subunit gamma-2 / Gamma-2-globin / Hb F Ggamma / Hemoglobin gamma-2 chain / Hemoglobin gamma-G chain


Mass: 16049.292 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBB, HBG2 / Production host: Escherichia coli (E. coli) / References: UniProt: P69892
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.15 Å3/Da / Density % sol: 42.84 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 1.9M Sodium/Potassium Phosphate, Batch method, pH 7, EVAPORATION, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.92→100 Å / Num. obs: 50708 / % possible obs: 93.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 35.6 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 17.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.92-1.952.90.417195.9
1.95-1.992.90.344196.7
1.99-2.0330.287195.7
2.03-2.072.90.213195.1
2.07-2.112.90.186195.3
2.11-2.1630.16195
2.16-2.2230.131195.1
2.22-2.282.90.127196.1
2.28-2.3430.105194.2
2.34-2.4230.095195.5
2.42-2.512.90.084195.4
2.51-2.612.90.078195.6
2.61-2.722.80.073193.7
2.72-2.872.80.062195.8
2.87-3.052.80.053194.6
3.05-3.282.70.046192
3.28-3.612.70.041191.5
3.61-4.142.60.038189.3
4.14-5.212.70.038188.1
5.21-1002.70.038182.5

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.242→45.073 Å / Occupancy max: 1 / Occupancy min: 0.53 / SU ML: 0.26 / σ(F): 1.36 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2322 1980 3.88 %
Rwork0.1746 --
obs0.1769 48746 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.6798 Å2
Refinement stepCycle: LAST / Resolution: 2.242→45.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8730 0 356 284 9370
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089373
X-RAY DIFFRACTIONf_angle_d1.09212805
X-RAY DIFFRACTIONf_dihedral_angle_d13.6563199
X-RAY DIFFRACTIONf_chiral_restr0.0681397
X-RAY DIFFRACTIONf_plane_restr0.0041580
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.242-2.27040.29441360.21913547X-RAY DIFFRACTION97
2.2704-2.30030.29891440.20893485X-RAY DIFFRACTION100
2.3003-2.33180.27791480.20833509X-RAY DIFFRACTION100
2.3318-2.36510.26331500.19813691X-RAY DIFFRACTION100
2.3651-2.40040.25181440.19123504X-RAY DIFFRACTION100
2.4004-2.43790.24361400.1963472X-RAY DIFFRACTION100
2.4379-2.47790.27421410.19963632X-RAY DIFFRACTION100
2.4779-2.52060.24971410.20413574X-RAY DIFFRACTION100
2.5206-2.56640.32811430.2113507X-RAY DIFFRACTION100
2.5664-2.61580.27431350.19233584X-RAY DIFFRACTION100
2.6158-2.66920.27411440.20443521X-RAY DIFFRACTION100
2.6692-2.72720.27391440.19673554X-RAY DIFFRACTION100
2.7272-2.79060.26211490.19023542X-RAY DIFFRACTION100
2.7906-2.86040.24161390.1863556X-RAY DIFFRACTION100
2.8604-2.93770.25881460.19313557X-RAY DIFFRACTION100
2.9377-3.02420.28171470.19863543X-RAY DIFFRACTION100
3.0242-3.12170.28741460.19773578X-RAY DIFFRACTION100
3.1217-3.23330.27521480.18153531X-RAY DIFFRACTION100
3.2333-3.36270.23971390.18373531X-RAY DIFFRACTION100
3.3627-3.51570.21541420.16493589X-RAY DIFFRACTION100
3.5157-3.7010.20191440.14383550X-RAY DIFFRACTION100
3.701-3.93270.17621450.13613509X-RAY DIFFRACTION100
3.9327-4.23610.18651430.13793540X-RAY DIFFRACTION99
4.2361-4.66210.21370.13063511X-RAY DIFFRACTION99
4.6621-5.33570.16711430.15063529X-RAY DIFFRACTION99
5.3357-6.71890.24781390.18793517X-RAY DIFFRACTION99
6.7189-45.0820.19551300.18993139X-RAY DIFFRACTION89
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5578-0.121-1.02653.0749-0.92793.81550.1271-0.15290.43030.07060.01450.0957-0.223-0.0193-0.09190.1673-0.00710.02420.1856-0.00270.2445-40.559811.00163.8019
23.74480.6801-0.32422.89621.28753.2170.17130.1381-0.0543-0.00510.0585-0.26280.16550.2689-0.18530.19250.0341-0.01410.26040.00730.1636-23.38895.9291-12.9402
32.6592-0.1357-0.50792.6630.81222.91920.0478-0.06730.2709-0.10970.0072-0.0849-0.20980.0597-0.04220.1286-0.02020.02160.18610.02220.20389.042110.127-53.3337
43.5327-0.3384-1.17323.3798-0.8792.2321-0.0151-0.1872-0.22070.09120.14180.40580.1857-0.1924-0.11190.2023-0.0192-0.03570.33280.05240.1916-7.31264.4044-36.2782
53.14190.5560.05013.19540.03714.3467-0.1331-0.02110.4423-0.26020.08090.2234-0.99850.44920.00470.4475-0.1021-0.01440.2372-0.03040.2512-12.150313.718516.1942
64.5149-0.4616-1.14882.27860.30944.3163-0.14750.2587-0.5039-0.01140.02650.16750.62520.08080.09470.32370.01930.04520.1751-0.02810.2903-18.3512-9.43813.5128
73.5502-1.66250.89544.4286-0.61373.1927-0.24190.12680.58670.3067-0.1112-0.5839-0.49610.12990.1690.2954-0.0333-0.09050.18550.05950.2884-19.100314.0204-64.5696
84.43580.3566-0.67672.4925-0.32952.54750.0403-0.0825-0.5476-0.0185-0.0427-0.18050.3932-0.00550.02170.2725-0.0416-0.03620.17760.00890.2486-13.6723-9.5377-63.86
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H

+
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://pdbjlvh1.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