[English] 日本語
Yorodumi
- PDB-6aw9: 2.55A resolution structure of SAH bound catechol O-methyltransfer... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6aw9
Title2.55A resolution structure of SAH bound catechol O-methyltransferase (COMT) L136M from Nannospalax galili
ComponentsCatechol O-methyltransferase
KeywordsTRANSFERASE / Spalax / COMT / S-adenosylmethionine binding
Function / homology
Function and homology information


catecholamine catabolic process / catechol O-methyltransferase activity / catechol O-methyltransferase / developmental process / dopamine metabolic process / methylation / axon / dendrite / magnesium ion binding / plasma membrane
Similarity search - Function
Catechol O-methyltransferase, eukaryotic / Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Catechol O-methyltransferase
Similarity search - Component
Biological speciesNannospalax galili (Upper Galilee mountains blind mole rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsLovell, S. / Mehzabeen, N. / Battaile, K.P. / Deng, Y. / Hanzlik, R.P. / Shams, I. / Moskovitz, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30 GM110761 United States
CitationJournal: To be published
Title: Crystal structure of the catechol-o-methyl transferase (COMT) enzyme of the subterranean mole rat (Spalax) and the effect of L136M substitution
Authors: Deng, Y. / Lovell, S. / Mehzabeen, N. / Battaile, K.P. / Hanzlik, R.P. / Shams, I. / Moskovitz, J.
History
DepositionSep 5, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Catechol O-methyltransferase
B: Catechol O-methyltransferase
C: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,4809
Polymers77,2063
Non-polymers1,2736
Water61334
1
A: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1603
Polymers25,7351
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1603
Polymers25,7351
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Catechol O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1603
Polymers25,7351
Non-polymers4242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.297, 102.410, 125.588
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Catechol O-methyltransferase / COMT


Mass: 25735.410 Da / Num. of mol.: 3 / Fragment: M43-P262 / Mutation: L136M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nannospalax galili (Upper Galilee mountains blind mole rat)
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A452CSQ2*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / 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: 2.64 Å3/Da / Density % sol: 53.34 % / Mosaicity: 0.14 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 14.4 % (w/v) PEG 8000, 80 mM sodium cacodylate, 160 mM calcium chloride, 20% glycerol

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.55→49.49 Å / Num. obs: 27248 / % possible obs: 99.7 % / Redundancy: 6.6 % / Biso Wilson estimate: 52.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Net I/σ(I): 11.7 / Num. measured all: 179065 / Scaling rejects: 0
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.2 / Num. measured all: 21344 / Num. unique all: 3260 / CC1/2: 0.791 / Net I/σ(I) obs: 1.5 / % possible all: 99.4

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.76 Å47.42 Å
Translation6.76 Å47.42 Å

-
Processing

Software
NameVersionClassification
Aimless0.5.25data scaling
PHASER2.6.1phasing
PHENIX(dev_2510: ???)refinement
PDB_EXTRACT3.22data extraction
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZLB

2zlb


Resolution: 2.55→44.579 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 32.72
RfactorNum. reflection% reflection
Rfree0.2588 1370 5.04 %
Rwork0.2075 --
obs0.2103 27176 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 166.27 Å2 / Biso mean: 70.9638 Å2 / Biso min: 34.25 Å2
Refinement stepCycle: final / Resolution: 2.55→44.579 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4870 0 81 34 4985
Biso mean--62.97 57.86 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025047
X-RAY DIFFRACTIONf_angle_d0.5656872
X-RAY DIFFRACTIONf_chiral_restr0.04796
X-RAY DIFFRACTIONf_plane_restr0.003878
X-RAY DIFFRACTIONf_dihedral_angle_d11.5543046
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.64110.42371390.32652519265899
2.6411-2.74690.41241280.29532554268299
2.7469-2.87190.36281230.28772541266499
2.8719-3.02320.36251240.27782545266999
3.0232-3.21260.29771430.235425482691100
3.2126-3.46060.31181190.215825752694100
3.4606-3.80870.21211390.19662574271399
3.8087-4.35940.2211740.171925712745100
4.3594-5.49080.19921510.16526082759100
5.4908-44.58560.25881300.19812771290199

+
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