[English] 日本語
Yorodumi
- PDB-9ihs: Microbial transglutaminase mutant - D3C/G283C -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ihs
TitleMicrobial transglutaminase mutant - D3C/G283C
ComponentsProtein-glutamine gamma-glutamyltransferase
KeywordsTRANSFERASE / transglutaminase / thermostable mutant / disulfide bond
Function / homologyProtein-glutamine gamma-glutamyltransferase / Protein-glutamine gamma-glutamyltransferase superfamily / Microbial transglutaminase / protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / Papain-like cysteine peptidase superfamily / DI(HYDROXYETHYL)ETHER / Protein-glutamine gamma-glutamyltransferase
Function and homology information
Biological speciesStreptomyces mobaraensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSuzuki, M. / Date, M. / Kashiwagi, T. / Takahashi, K. / Nakamura, A. / Tanokura, M. / Suzuki, E. / Yokoyama, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Ajinomoto Co., Inc. Japan
Development of Systems and Technology for Advanced Measurement and Analysis (Program-S)-Fund of the Japan Science and Technology Agency Japan
CitationJournal: Appl.Microbiol.Biotechnol. / Year: 2024
Title: Random mutagenesis and disulfide bond formation improved thermostability in microbial transglutaminase.
Authors: Suzuki, M. / Date, M. / Kashiwagi, T. / Takahashi, K. / Nakamura, A. / Tanokura, M. / Suzuki, E. / Yokoyama, K.
History
DepositionJun 18, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein-glutamine gamma-glutamyltransferase
B: Protein-glutamine gamma-glutamyltransferase
C: Protein-glutamine gamma-glutamyltransferase
D: Protein-glutamine gamma-glutamyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,83913
Polymers151,8104
Non-polymers1,0299
Water19,9251106
1
A: Protein-glutamine gamma-glutamyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1833
Polymers37,9531
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area15740 Å2
MethodPISA
2
B: Protein-glutamine gamma-glutamyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2894
Polymers37,9531
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area15940 Å2
MethodPISA
3
C: Protein-glutamine gamma-glutamyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1833
Polymers37,9531
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-11 kcal/mol
Surface area15540 Å2
MethodPISA
4
D: Protein-glutamine gamma-glutamyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1833
Polymers37,9531
Non-polymers2312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area15600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.760, 117.360, 85.470
Angle α, β, γ (deg.)90.000, 113.028, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Protein-glutamine gamma-glutamyltransferase / MTG / Transglutaminase / TGase


Mass: 37952.562 Da / Num. of mol.: 4 / Mutation: D3C,G283C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces mobaraensis (bacteria) / Production host: Corynebacterium glutamicum (bacteria)
References: UniProt: P81453, protein-glutamine gamma-glutamyltransferase
#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1106 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25 w/v% polyethylene glycol 1000, 100 mM MES-NaOH buffer (pH5.0), and 25 mM CaCl2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→78.659 Å / Num. obs: 93774 / % possible obs: 97.1 % / Redundancy: 3.8288 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 24.04
Reflection shellResolution: 2→2.2 Å / Rmerge(I) obs: 0.143 / Num. unique obs: 22950

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.08 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.3 / SU ML: 0.121 / Cross valid method: FREE R-VALUE / ESU R: 0.199 / ESU R Free: 0.176 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2345 4694 5.009 %
Rwork0.1807 89024 -
all0.183 --
obs-93718 97.215 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 30.099 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å2-0.147 Å2
2--0.014 Å20 Å2
3----0.065 Å2
Refinement stepCycle: LAST / Resolution: 2→47.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10712 0 59 1106 11877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01211087
X-RAY DIFFRACTIONr_angle_refined_deg1.5791.65215002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85451322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.61320.987750
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.921151743
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.44515121
X-RAY DIFFRACTIONr_chiral_restr0.1160.21301
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029001
X-RAY DIFFRACTIONr_nbd_refined0.2170.25574
X-RAY DIFFRACTIONr_nbtor_refined0.3140.27447
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.21075
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2110.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1720.229
X-RAY DIFFRACTIONr_mcbond_it2.4282.7865294
X-RAY DIFFRACTIONr_mcangle_it3.4214.1666611
X-RAY DIFFRACTIONr_scbond_it3.1633.0725793
X-RAY DIFFRACTIONr_scangle_it4.5864.4718390
X-RAY DIFFRACTIONr_lrange_it6.40338.07818004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.2823160.216381X-RAY DIFFRACTION94.4836
2.052-2.1080.273330.1966362X-RAY DIFFRACTION96.595
2.108-2.1690.2733270.1996180X-RAY DIFFRACTION96.6434
2.169-2.2360.2783430.1946014X-RAY DIFFRACTION96.9055
2.236-2.3090.2612870.185862X-RAY DIFFRACTION96.8652
2.309-2.390.2522960.1845692X-RAY DIFFRACTION97.4134
2.39-2.480.2472980.1915425X-RAY DIFFRACTION97.2472
2.48-2.5810.2682960.1835261X-RAY DIFFRACTION97.2864
2.581-2.6960.282740.1925086X-RAY DIFFRACTION97.7567
2.696-2.8280.2512410.1964877X-RAY DIFFRACTION97.6531
2.828-2.980.2642250.1944636X-RAY DIFFRACTION97.9843
2.98-3.1610.2412200.1964398X-RAY DIFFRACTION97.5909
3.161-3.3790.2252220.194113X-RAY DIFFRACTION98.3439
3.379-3.6490.2232280.1843808X-RAY DIFFRACTION98.1279
3.649-3.9960.2041810.1563574X-RAY DIFFRACTION98.247
3.996-4.4660.1791580.1463232X-RAY DIFFRACTION98.2609
4.466-5.1550.1951540.1532836X-RAY DIFFRACTION98.3553
5.155-6.3060.221380.1852402X-RAY DIFFRACTION98.2972
6.306-8.890.2021040.1661880X-RAY DIFFRACTION98.4127
8.89-47.080.214530.1881005X-RAY DIFFRACTION92.2406

+
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