[English] 日本語
Yorodumi
- PDB-3o89: Crystal Structure of Sperm Whale Myoglobin G65T -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3o89
TitleCrystal Structure of Sperm Whale Myoglobin G65T
ComponentsMyoglobin
KeywordsOXYGEN STORAGE
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Globin / Myoglobin / Globin-like superfamily / Globin/Protoglobin / Globin / Globins / Globin-like / Orthogonal Bundle / Mainly Alpha
Myoglobin
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsHuang, X. / Lovelace, L. / Lebioda, L.
CitationJournal: TO BE PUBLISHED
Title: Investigations of Structural Factors that Influence the Mechanism of Halophenol Dehalogenation using 'Peroxidase-Like' Myoglobin mutants and 'Myoglobin-Like' Amphitrite ornata Dehaloperoxidase Mutants
Authors: Huang, X. / Du, J. / Dawson, J. / Lebioda, L.
Validation Report
SummaryFull reportAbout validation report
History
DepositionAug 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0884
Polymers17,2791
Non-polymers8093
Water4,378243
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)90.439, 90.439, 45.247
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6

-
Components

#1: Protein/peptide Myoglobin /


Mass: 17279.004 Da / Num. of mol.: 1 / Mutation: G65T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / 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 / Heme
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Sulfate
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O / Water

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.21 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5
Details: 2.6M AS, 50mM Tris 8.5, 1mM EDTA, EVAPORATION, temperature 293K

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. obs: 87374 / % possible obs: 88.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.049 / Χ2: 1.95 / Net I/σ(I): 17.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.05-1.071.10.5567110.7714.6
1.07-1.091.30.46118340.89337
1.09-1.111.50.4229460.93160.5
1.11-1.131.90.36538720.94979
1.13-1.162.40.30545040.95892.8
1.16-1.182.80.26247791.00397.5
1.18-1.2130.23648330.99898.4
1.21-1.2430.21248781.06399.1
1.24-1.2830.17948381.07999.5
1.28-1.3230.14849291.07199.7
1.32-1.373.10.13148951.1199.7
1.37-1.433.10.11548941.27199.8
1.43-1.493.10.09548841.36499.9
1.49-1.573.10.07149321.289100
1.57-1.674.10.07649181.506100
1.67-1.84.80.07748952.16899.9
1.8-1.9860.06849682.697100
1.98-2.266.10.05149522.76499.9
2.26-2.856.10.04249522.92299.8
2.85-505.90.03549602.87897.7

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-3000data collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→31.99 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.185 / WRfactor Rwork: 0.1741 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.9171 / SU B: 0.701 / SU ML: 0.016 / SU R Cruickshank DPI: 0.0297 / SU Rfree: 0.0285 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1829 4156 5 %RANDOM
Rwork0.1721 ---
Obs0.1727 83174 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 308.85 Å2 / Biso mean: 15.258 Å2 / Biso min: 5.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.1→31.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1219 0 53 243 1515
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0060.0221305
r_angle_refined_deg1.0342.0611770
r_dihedral_angle_1_deg4.6065152
r_dihedral_angle_2_deg33.8524.25954
r_dihedral_angle_3_deg12.14615237
r_dihedral_angle_4_deg11.59154
r_chiral_restr0.0740.2184
r_gen_planes_refined0.0040.02954
r_nbd_refined0.2010.2661
r_nbtor_refined0.3040.2879
r_xyhbond_nbd_refined0.0720.2188
r_symmetry_vdw_refined0.1950.231
r_symmetry_hbond_refined0.0910.222
r_mcbond_it0.7681.5773
r_mcangle_it1.26421209
r_scbond_it1.9623592
r_scangle_it2.9464.5559
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 241 -
Rwork0.32 4475 -
All-4716 -
Obs--75.12 %
Refinement TLS params.Method: refined / Origin x: 25.565 Å / Origin y: -23.469 Å / Origin z: 0.578 Å
111213212223313233
T-0.0092 Å2-0.0066 Å2-0.0016 Å2-0.0043 Å2-0.0042 Å2--0 Å2
L0.1731 °20.0577 °20.1435 °2-0.0635 °20.0296 °2--0.1264 °2
S-0.0143 Å °-0.0522 Å °0.0056 Å °-0.0114 Å °0.0007 Å °0.0272 Å °0.0397 Å °-0.0346 Å °0.0137 Å °
Refinement TLS group

Refinement-ID: X-RAY DIFFRACTION / Refine TLS-ID: 1 / Auth asym-ID: A

IDAuth seq-ID
12001 - 2157
24001 - 4256

+
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