[English] 日本語
Yorodumi
- PDB-107m: SPERM WHALE MYOGLOBIN V68F N-BUTYL ISOCYANIDE AT PH 9.0 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 107m
TitleSPERM WHALE MYOGLOBIN V68F N-BUTYL ISOCYANIDE AT PH 9.0
ComponentsMYOGLOBIN
KeywordsOXYGEN TRANSPORT / LIGAND BINDING / OXYGEN STORAGE / OXYGEN BINDING / HEME
Function / homologyGlobin / Myoglobin / Globin-like superfamily / Globin/Protoglobin / Globin / Globin family profile. / oxygen carrier activity / oxygen binding / heme binding / metal ion binding / Myoglobin
Function and homology information
Specimen sourcePhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 2.09 Å resolution
AuthorsSmith, R.D. / Olson, J.S. / Phillips Jr., G.N.
CitationJournal: Thesis, Rice / Year: 1999
Title: Correlations between Bound N-Alkyl Isocyanide Orientations and Pathways for Ligand Binding in Recombinant Myoglobins
Authors: Smith, R.D.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 22, 1997 / Release: Apr 8, 1998
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 8, 1998Structure modelrepositoryInitial release
1.1Mar 24, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Mar 7, 2018Structure modelData collection / Otherdiffrn_source / pdbx_database_status_diffrn_source.source / _pdbx_database_status.process_site

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MYOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2094
Polyers17,4131
Non-polymers7963
Water2,432135
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)91.798, 91.798, 45.911
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP 6

-
Components

#1: Protein/peptide MYOGLOBIN /


Mass: 17413.205 Da / Num. of mol.: 1 / Mutation: INS(M0), V68F, D122N / Source: (gene. exp.) Physeter catodon (sperm whale) / Genus: Physeter / Tissue: SKELETAL MUSCLE / Cellular location: CYTOPLASM / Organ: SKELETALSkeleton / Plasmid name: PEMBL 19+ / Genus (production host): Escherichia / Production host: Escherichia coli (E. coli) / Strain (production host): PHAGE RESISTANT TB1 / References: UniProt: P02185
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Formula: SO4 / Sulfate
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Formula: C34H32FeN4O4 / Heme
#4: Chemical ChemComp-NBN / N-BUTYL ISOCYANIDE


Mass: 83.132 Da / Num. of mol.: 1 / Formula: C5H9N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 / Density percent sol: 60.1 %
Crystal growpH: 9
Details: 3.0 M AMMONIUM SULFATE, 20 MM TRIS, 1MM EDTA, PH 9.0

-
Data collection

DiffractionMean temperature: 292 kelvins
SourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: RIGAKU / Details: PINHOLE COLLIMATOR / Detector: IMAGE PLATE / Collection date: Mar 1, 1997
RadiationMonochromator: GRAPHITE(002) / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 17.8 Å2 / D resolution high: 2.09 Å / D resolution low: 6 Å / Number obs: 12167 / Observed criterion sigma I: 0 / Rmerge I obs: 0.069 / Redundancy: 4.63 % / Percent possible obs: 91.7
Reflection shellRmerge I obs: 0.264 / Highest resolution: 2.09 Å / Lowest resolution: 2.1 Å / Redundancy: 4.26 % / Percent possible all: 94.5

-
Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.851phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SPERM WHALE MYOGLOBIN 0M, D122N (DEOXY)

R Free selection details: RANDOM / Data cutoff high absF: 1 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Sigma F: 0
Displacement parametersB iso mean: 29 Å2
Least-squares processR factor R free: 0.23 / R factor R free error: 0.007 / R factor R work: 0.167 / R factor obs: 0.167 / Highest resolution: 2.09 Å / Lowest resolution: 5 Å / Number reflection R free: 1091 / Number reflection obs: 10936 / Percent reflection R free: 1 / Percent reflection obs: 89.3
Refine analyzeLuzzati coordinate error free: 0.27 Å / Luzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a free: 0.24 Å / Luzzati sigma a obs: 0.22 Å
Refine hist #LASTHighest resolution: 2.09 Å / Lowest resolution: 5 Å
Number of atoms included #LASTProtein: 1229 / Nucleic acid: 0 / Ligand: 49 / Solvent: 140 / Total: 1418
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d18.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.21
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.161.50
X-RAY DIFFRACTIONx_mcangle_it3.972.00
X-RAY DIFFRACTIONx_scbond_it7.892.50
X-RAY DIFFRACTIONx_scangle_it11.622.50
Refine LS shellHighest resolution: 2.09 Å / R factor R free: 0.262 / R factor R free error: 0.023 / R factor R work: 0.237 / Lowest resolution: 2.18 Å / Number reflection R free: 126 / Number reflection R work: 1195 / Total number of bins used: 8 / Percent reflection R free: 9.5 / Percent reflection obs: 85.8
Xplor file
Refine IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAMETER.HEMETOPOLOGY.HEME
X-RAY DIFFRACTION3PARAMETER.NBNCTOPOLOGY.NBNC
X-RAY DIFFRACTION4PARAM19.SOLVTOPH19.SOLV

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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