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- PDB-7c9j: Transglutaminase from Geobacillus stearothermophilus (without C-t... -

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Basic information

Entry
Database: PDB / ID: 7c9j
TitleTransglutaminase from Geobacillus stearothermophilus (without C-terminal extension)
ComponentsProtein-glutamine gamma-glutamyltransferase
KeywordsTRANSFERASE / Transglutaminase
Function / homologyProtein-glutamine gamma-glutamyltransferase, bacteria / Protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / CITRIC ACID / Protein-glutamine gamma-glutamyltransferase
Function and homology information
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsTakita, T. / Mikami, B. / Lei, Y. / Jing, Y. / Yamada, A. / Yasukawa, K.
CitationJournal: To be published
Title: Transglutaminase from Geobacillus stearothermophilus (without C-terminal extension)
Authors: Takita, T. / Mikami, B. / Lei, Y. / Jing, Y. / Yamada, A. / Yamada, A.
History
DepositionJun 6, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 9, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-glutamine gamma-glutamyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6337
Polymers29,1311
Non-polymers5026
Water1,56787
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)94.090, 94.090, 158.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-471-

HOH

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Components

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


Mass: 29130.971 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: D9548_14210 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A3L7D5Y5, protein-glutamine gamma-glutamyltransferase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG 20000, 2-(N-morpholino)ethanesulfonic acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Dec 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 15940 / % possible obs: 98.6 % / Redundancy: 5.8 % / Biso Wilson estimate: 44.88 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.047 / Net I/σ(I): 21.16
Reflection shellResolution: 2.1→2.22 Å / Redundancy: 2.98 % / Rmerge(I) obs: 0.517 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 4544 / CC1/2: 0.743 / Rrim(I) all: 0.618 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4P8I

4p8i


Resolution: 2.1→39.45 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2136 797 5 %
Rwork0.1862 --
obs0.1876 15935 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→39.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1678 0 33 87 1798
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091818
X-RAY DIFFRACTIONf_angle_d0.9832463
X-RAY DIFFRACTIONf_dihedral_angle_d9.794252
X-RAY DIFFRACTIONf_chiral_restr0.055260
X-RAY DIFFRACTIONf_plane_restr0.006321
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.230.23961240.212372X-RAY DIFFRACTION95
2.23-2.40.23561320.19332500X-RAY DIFFRACTION100
2.4-2.640.25111330.19942520X-RAY DIFFRACTION100
2.64-3.020.25811340.20422555X-RAY DIFFRACTION100
3.02-3.810.20841340.19012545X-RAY DIFFRACTION100
3.81-39.450.1921400.17322646X-RAY DIFFRACTION100

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