[English] 日本語
Yorodumi
- PDB-2dut: Crystal structure of a M-loop deletion variant of MENT in the nat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2dut
TitleCrystal structure of a M-loop deletion variant of MENT in the native conformation
ComponentsHeterochromatin-associated protein MENT
KeywordsHYDROLASE INHIBITOR / SERINE PROTEASE INHIBITOR / SERPIN
Function / homology
Function and homology information


nucleate erythrocyte maturation / chromosome condensation / serine-type endopeptidase inhibitor activity / chromatin DNA binding / chromatin organization / chromatin / extracellular space / nucleoplasm
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Heterochromatin-associated protein MENT
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWhisstock, J.C. / Buckle, A.M. / McGowan, S. / Irving, J.A.
CitationJournal: Embo J. / Year: 2006
Title: X-ray crystal structure of MENT: evidence for functional loop-sheet polymers in chromatin condensation
Authors: McGowan, S. / Buckle, A.M. / Irving, J.A. / Ong, P.C. / Bashtannyk-Puhalovich, T.A. / Kan, W.T. / Henderson, K.N. / Bulynko, Y.A. / Popova, E.Y. / Smith, A.I. / Bottomley, S.P. / Rossjohn, J. ...Authors: McGowan, S. / Buckle, A.M. / Irving, J.A. / Ong, P.C. / Bashtannyk-Puhalovich, T.A. / Kan, W.T. / Henderson, K.N. / Bulynko, Y.A. / Popova, E.Y. / Smith, A.I. / Bottomley, S.P. / Rossjohn, J. / Grigoryev, S.A. / Pike, R.N. / Whisstock, J.C.
History
DepositionJul 26, 2006Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 8, 2006ID: 2H4S
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heterochromatin-associated protein MENT
B: Heterochromatin-associated protein MENT
C: Heterochromatin-associated protein MENT
D: Heterochromatin-associated protein MENT


Theoretical massNumber of molelcules
Total (without water)195,4244
Polymers195,4244
Non-polymers00
Water2,450136
1
A: Heterochromatin-associated protein MENT


Theoretical massNumber of molelcules
Total (without water)48,8561
Polymers48,8561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heterochromatin-associated protein MENT


Theoretical massNumber of molelcules
Total (without water)48,8561
Polymers48,8561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heterochromatin-associated protein MENT


Theoretical massNumber of molelcules
Total (without water)48,8561
Polymers48,8561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Heterochromatin-associated protein MENT


Theoretical massNumber of molelcules
Total (without water)48,8561
Polymers48,8561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.559, 182.559, 96.723
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
Heterochromatin-associated protein MENT / MENT


Mass: 48855.910 Da / Num. of mol.: 4 / Mutation: deletion mutant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: MENT-1 / Plasmid: pBAD-HisA / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: O73790
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 4.76 Å3/Da / Density % sol: 74.16 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 1.7-1.9M AMMONIUM SULFATE, 0.1M SODIUM ACETATE, PH4.3-4.45, VAPOR DIFFUSION, HANGING DROP, temperature 290K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. all: 71951 / Num. obs: 68817 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.5 %
Rfree details: Random selection of twin-related reflection pairs
Rmerge(I) obs: 0.114 / Net I/σ(I): 10.8
Reflection shellResolution: 3→3.1 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
ADSCdata collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1OVA

1ova


Resolution: 3→20 Å / Redundancy reflection obs: 2.5 / Data cutoff high absF: 0 / Data cutoff low absF: 0 / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: THE DATA IS TWINNED. THE TWINNING OPERATOR IS (H,K,L)-> (H+K,-K,-L) AND THE ESTIMATED PARTIAL TWINNING FRACTION IS 0.44. THE TWINNED R-FACTORS ARE 29.7% (OBS), 29.7%(WORK) AND 32.4%(FREE). ...Details: THE DATA IS TWINNED. THE TWINNING OPERATOR IS (H,K,L)-> (H+K,-K,-L) AND THE ESTIMATED PARTIAL TWINNING FRACTION IS 0.44. THE TWINNED R-FACTORS ARE 29.7% (OBS), 29.7%(WORK) AND 32.4%(FREE). THE TWINNED BIN R-FACTORS ARE 36.0(WORK) AND 37.0(FREE). AT THIS TWINNING FRACTION, THE ESTIMATE IS LIKELY TO BE INACCURATE. HENCE, THE DATA WAS ARTIFICIALLY PERFECTLY TWINNED (=0.5) BY AVERAGING TWIN- RELATED REFLECTIONS. TO AVOID TEST-SET BIAS, TWIN-RELATED REFLECTIONS WERE RANDOMLY SELECTED IN PAIRS AND EXCLUDED FROM REFINEMENT FOR THE CALCULATION OF RFREE. CYCLES OF RIGID BODY REFINEMENT, SIMULATED ANNEALING, B-FACTOR REFINEMENT AND MAP BUILDING WERE UNDERTAKEN IN CNS USING THE XTAL_TWIN SUITE OF SCRIPTS.IN ORDER TO MAXIMISE THE OBSERVATION-TO-PARAMETER RATIO, STRICT CONSTRAINTS WERE APPLIED DURING REFINEMENT WITH CNS; AS SUCH, THE FOUR CHAINS ARE IDENTICAL AND RELATED PURELY BY COORDINATE TRANSFORMATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.293 3090 -RANDOM
Rwork0.278 ---
obs0.278 68817 95.6 %-
all-71951 --
Solvent computationSolvent model: BULK / Bsol: 65.27 Å2 / ksol: 0.282 e/Å3
Displacement parametersBiso max: 103.164 Å2 / Biso mean: 41.015 Å2 / Biso min: 18.1339 Å2
Baniso -1Baniso -2Baniso -3
1--0.221 Å2-7.434 Å20 Å2
2---0.221 Å20 Å2
3---0.443 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10884 0 0 136 11020
LS refinement shellResolution: 3→3.1 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.35 384 5.4 %
Rwork0.334 --
all-7176 -
obs-7097 98.9 %

+
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://pdbjlvh1.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