[English] 日本語
Yorodumi
- PDB-2xzz: Crystal structure of the human transglutaminase 1 beta-barrel domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xzz
TitleCrystal structure of the human transglutaminase 1 beta-barrel domain
ComponentsPROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE K
KeywordsTRANSFERASE
Function / homology
Function and homology information


: / cell envelope organization / cornification / protein-glutamine gamma-glutamyltransferase / positive regulation of keratinocyte proliferation / protein-glutamine gamma-glutamyltransferase activity / protein modification process => GO:0036211 / Formation of the cornified envelope / peptide cross-linking / cornified envelope ...: / cell envelope organization / cornification / protein-glutamine gamma-glutamyltransferase / positive regulation of keratinocyte proliferation / protein-glutamine gamma-glutamyltransferase activity / protein modification process => GO:0036211 / Formation of the cornified envelope / peptide cross-linking / cornified envelope / positive regulation of cell cycle / keratinocyte differentiation / extracellular exosome / membrane / identical protein binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues ...Transglutaminase, N-terminal / Transglutaminase, C-terminal / Transglutaminase, active site / Protein-glutamine gamma-glutamyltransferase, animal / Transglutaminase, C-terminal domain superfamily / Transglutaminase family / Transglutaminase family, C-terminal ig like domain / Transglutaminases active site. / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Transglutaminase-like superfamily / Papain-like cysteine peptidase superfamily / Immunoglobulin E-set / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Protein-glutamine gamma-glutamyltransferase K
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVollmar, M. / Krysztofinska, E. / Krojer, T. / Yue, W.W. / Cooper, C. / Kavanagh, K. / Allerston, C. / Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. ...Vollmar, M. / Krysztofinska, E. / Krojer, T. / Yue, W.W. / Cooper, C. / Kavanagh, K. / Allerston, C. / Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
CitationJournal: To be Published
Title: Crystal Structure of the Human Transglutaminase 1 Beta-Barrel Domain
Authors: Vollmar, M. / Krysztofinska, E. / Krojer, T. / Yue, W.W. / Cooper, C. / Kavanagh, K. / Allerston, C. / Chaikuad, A. / von Delft, F. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Bountra, C. / Oppermann, U.
History
DepositionNov 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE K


Theoretical massNumber of molelcules
Total (without water)10,9931
Polymers10,9931
Non-polymers00
Water72140
1
A: PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE K
x 24


Theoretical massNumber of molelcules
Total (without water)263,82524
Polymers263,82524
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation24_555-z,-y,-x1
crystal symmetry operation8_555-z,x,-y1
Buried area60210 Å2
ΔGint-351.2 kcal/mol
Surface area92370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.740, 115.740, 115.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432

-
Components

#1: Protein PROTEIN-GLUTAMINE GAMMA-GLUTAMYLTRANSFERASE K / EPIDERMAL TGASE / TRANSGLUTAMINASE K / TRANSGLUTAMINASE-1 / TG(K) / TGK / TGASE K / TGASE-1


Mass: 10992.705 Da / Num. of mol.: 1 / Fragment: BETA BARREL DOMAIN, RESIDUES 693-787
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): R3-PRARE2
References: UniProt: P22735, protein-glutamine gamma-glutamyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSTARTING SER AND MET ARE DUE TO CLONING

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.19 % / Description: NONE
Crystal growDetails: 0.7 M (NH4)2SO4, 1% PEG3350, 0.1 M BIS-TRIS (PH 5.5)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.893
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.893 Å / Relative weight: 1
ReflectionResolution: 2.3→19.29 Å / Num. obs: 6155 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 10.8 % / Biso Wilson estimate: 54.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 21
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 4.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRUES 1EOX, 1FIE, 1GGY, 1G0D AND 1QRK IN AN ENSEMBLE

1eox

1fie

1ggy

1g0d

1qrk


Resolution: 2.3→19.29 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 14.551 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.26688 290 4.7 %RANDOM
Rwork0.21901 ---
obs0.22118 5852 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.281 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms705 0 0 40 745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022721
X-RAY DIFFRACTIONr_bond_other_d0.0040.02467
X-RAY DIFFRACTIONr_angle_refined_deg1.8291.998987
X-RAY DIFFRACTIONr_angle_other_deg0.95131161
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.096598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.4972524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.20215117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.862154
X-RAY DIFFRACTIONr_chiral_restr0.0990.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021797
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02123
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0023485
X-RAY DIFFRACTIONr_mcbond_other0.4543196
X-RAY DIFFRACTIONr_mcangle_it3.5875789
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1477236
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.7059197
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 18 -
Rwork0.372 417 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.2713-1.6856-0.76658.3275.2739.6018-0.136-0.18660.49290.4824-0.27860.3885-0.0112-0.18020.41460.0567-0.0425-0.00510.23950.00220.26478.0477-24.864433.9476
23.4328-2.0004-2.71924.22165.866113.59270.013-0.30050.5714-0.2660.2028-0.0048-0.7470.216-0.21580.1981-0.08350.02240.21640.02040.340712.2553-21.829929.9423
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 754
2X-RAY DIFFRACTION2A755 - 787

+
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