[English] 日本語
Yorodumi
- PDB-4f6b: Aquomet structure of His100Phe Cerebratulus lacteus mini-hemoglobin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f6b
TitleAquomet structure of His100Phe Cerebratulus lacteus mini-hemoglobin
ComponentsNeural hemoglobin
KeywordsOXYGEN TRANSPORT / oxygen-storage / apolar tunnel
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Neural hemoglobin
Similarity search - Component
Biological speciesCerebratulus lacteus (milky ribbon-worm)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.64 Å
AuthorsSoman, J. / Salter, M.D. / Olson, J.S.
CitationJournal: To be Published
Title: Aquomet structure of His100Phe Cerebratulus lacteus mini-hemoglobin
Authors: Soman, J. / Salter, M.D. / Olson, J.S.
History
DepositionMay 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: Neural hemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3614
Polymers11,5561
Non-polymers8053
Water2,666148
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.680, 43.470, 59.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Neural hemoglobin / NrHb


Mass: 11555.977 Da / Num. of mol.: 1 / Mutation: His100Phe
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cerebratulus lacteus (milky ribbon-worm)
Production host: Escherichia coli (E. coli) / References: UniProt: O76242
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 148 / 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: 2.39 Å3/Da / Density % sol: 48.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: Protein crystallized from 2.5 mM Ammonium Sulfate and 0.1M sodium Citrate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5412 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5412 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 13828 / % possible obs: 98 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.049 / Χ2: 1.343 / Net I/σ(I): 49.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.64-1.673.40.1126761.992198.1
1.67-1.73.50.1016791.919198.3
1.7-1.733.50.0876721.807198.4
1.73-1.773.50.0866551.734197.9
1.77-1.813.50.0836941.833197.5
1.81-1.853.40.0766801.652197.3
1.85-1.893.40.0716691.637197
1.89-1.943.30.0646671.619197.4
1.94-23.30.066671.405198.2
2-2.073.30.0567001.41197.8
2.07-2.143.20.0536831.225198.6
2.14-2.233.20.0516801.223198.1
2.23-2.333.20.0486911.129197.6
2.33-2.453.20.0517081.14199.4
2.45-2.63.20.0516851.064198.7
2.6-2.83.30.0496960.957198.4
2.8-3.093.30.0497160.9198.5
3.09-3.533.30.0467130.774198.3
3.53-4.453.40.0457180.706198.6
4.45-503.30.0487790.737196.5

-
Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
d*TREKdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.64→24.545 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8827 / SU ML: 0.23 / σ(F): 1.34 / Phase error: 17.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2019 1379 10 %
Rwork0.1801 --
obs0.1823 13789 97.95 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.958 Å2 / ksol: 0.381 e/Å3
Displacement parametersBiso max: 50.56 Å2 / Biso mean: 18.6798 Å2 / Biso min: 5.97 Å2
Baniso -1Baniso -2Baniso -3
1--0.8472 Å2-0 Å20 Å2
2---3.0707 Å20 Å2
3---3.9178 Å2
Refinement stepCycle: LAST / Resolution: 1.64→24.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms815 0 54 148 1017
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007904
X-RAY DIFFRACTIONf_angle_d0.9431235
X-RAY DIFFRACTIONf_chiral_restr0.069119
X-RAY DIFFRACTIONf_plane_restr0.004157
X-RAY DIFFRACTIONf_dihedral_angle_d14.8300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6404-1.6990.31071350.30211208134397
1.699-1.7670.28631330.24051195132898
1.767-1.84740.2611370.21611232136997
1.8474-1.94470.19521340.17871203133797
1.9447-2.06650.18791360.16821226136298
2.0665-2.2260.18581370.16431232136998
2.226-2.44980.18231400.17151254139499
2.4498-2.80390.19051380.18051241137999
2.8039-3.53090.20741430.17821278142198
3.5309-24.54810.18861460.16521341148798
Refinement TLS params.Method: refined / Origin x: 30.6975 Å / Origin y: 35.8164 Å / Origin z: 10.5637 Å
111213212223313233
T0.0684 Å2-0.0034 Å20.0005 Å2-0.0893 Å20.0011 Å2--0.0814 Å2
L0.4003 °20.2391 °2-0.6015 °2-0.7054 °2-0.1412 °2--0.9945 °2
S0.0005 Å °-0.0459 Å °0.024 Å °0.0295 Å °0.018 Å °-0.0168 Å °0.011 Å °0.1309 Å °-0.0191 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA0 - 1112
2X-RAY DIFFRACTION1allA1 - 448

+
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