[English] 日本語
Yorodumi
- PDB-3h57: Myoglobin Cavity Mutant H64LV68N Deoxy form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3h57
TitleMyoglobin Cavity Mutant H64LV68N Deoxy form
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / OXYGEN TRANSPORT / Myoglobin / active site hydration / ligand entry and exit / oxygen storage and transport / Heme / Iron / Metal-binding / Muscle protein / Transport
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsSoman, J. / Olson, J.S.
CitationJournal: J.Am.Chem.Soc. / Year: 2009
Title: Optical detection of disordered water within a protein cavity.
Authors: Goldbeck, R.A. / Pillsbury, M.L. / Jensen, R.A. / Mendoza, J.L. / Nguyen, R.L. / Olson, J.S. / Soman, J. / Kliger, D.S. / Esquerra, R.M.
History
DepositionApr 21, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 13, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.3Sep 6, 2023Group: 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: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9722
Polymers17,3551
Non-polymers6161
Water5,819323
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.320, 90.320, 45.230
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein Myoglobin


Mass: 17355.146 Da / Num. of mol.: 1 / Mutation: H64L, V68N, D122N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): Phage resistant TB1 / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 3.07 Å3/Da / Density % sol: 59.92 %
Crystal growTemperature: 293 K / Method: batch method / pH: 9
Details: Protein Solution (20mg/ml protein in 0.02M Tris.HCl pH9.0) mixed with mother liquor (3.2M Ammonium Sulphate, 0.05M Tris.HCl, pH9.0) for final concentrations of 2.5M Ammonium Sulphate, Batch ...Details: Protein Solution (20mg/ml protein in 0.02M Tris.HCl pH9.0) mixed with mother liquor (3.2M Ammonium Sulphate, 0.05M Tris.HCl, pH9.0) for final concentrations of 2.5M Ammonium Sulphate, Batch Method, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 21, 2008
RadiationMonochromator: Multilayer / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.54→45.16 Å / Num. all: 31218 / Num. obs: 24865 / % possible obs: 79.6 % / Observed criterion σ(I): 3 / Redundancy: 3.9 % / Biso Wilson estimate: 15 Å2 / Rmerge(I) obs: 0.04 / Χ2: 0.95 / Net I/σ(I): 23.8 / Scaling rejects: 734
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 1.26 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 3.9 / Num. measured all: 715 / Num. unique all: 566 / Χ2: 0.42 / % possible all: 18.2

-
Processing

Software
NameVersionClassificationNB
d*TREK9.9.3Ldata processing
CNS1.1refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
CrystalCleardata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2mgl

2mgl


Resolution: 1.7→45.16 Å / Occupancy max: 1 / Occupancy min: 0.46 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 1066 4.6 %random
Rwork0.214 ---
all-22372 --
obs-22079 94.5 %-
Solvent computationBsol: 53.229 Å2
Displacement parametersBiso max: 90.09 Å2 / Biso mean: 16.792 Å2 / Biso min: 4.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.513 Å2-1.174 Å20 Å2
2---0.513 Å20 Å2
3---1.027 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.02 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.7→45.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 43 323 1589
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d17.8
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.279 152 -
Rwork0.247 --
obs-2862 77.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2CVheme.par
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param

+
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