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- PDB-1iu4: Crystal Structure Analysis of the Microbial Transglutaminase -

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Basic information

Entry
Database: PDB / ID: 1iu4
TitleCrystal Structure Analysis of the Microbial Transglutaminase
Componentsmicrobial transglutaminase
KeywordsTRANSFERASE / ALPHA-BETA
Function / homology
Function and homology information


protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity
Similarity search - Function
Microbial transglutaminase. Chain: a / Protein-glutamine gamma-glutamyltransferase / Protein-glutamine gamma-glutamyltransferase / Protein-glutamine gamma-glutamyltransferase superfamily / Microbial transglutaminase / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Protein-glutamine gamma-glutamyltransferase
Similarity search - Component
Biological speciesStreptomyces mobaraensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsKashiwagi, T. / Yokoyama, K. / Ishikawa, K. / Ono, K. / Ejima, D. / Matsui, H. / Suzuki, E.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of microbial transglutaminase from Streptoverticillium mobaraense
Authors: Kashiwagi, T. / Yokoyama, K. / Ishikawa, K. / Ono, K. / Ejima, D. / Matsui, H. / Suzuki, E.
History
DepositionFeb 27, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: microbial transglutaminase
B: microbial transglutaminase
C: microbial transglutaminase
D: microbial transglutaminase


Theoretical massNumber of molelcules
Total (without water)151,6744
Polymers151,6744
Non-polymers00
Water9,908550
1
A: microbial transglutaminase


Theoretical massNumber of molelcules
Total (without water)37,9181
Polymers37,9181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: microbial transglutaminase


Theoretical massNumber of molelcules
Total (without water)37,9181
Polymers37,9181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: microbial transglutaminase


Theoretical massNumber of molelcules
Total (without water)37,9181
Polymers37,9181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: microbial transglutaminase


Theoretical massNumber of molelcules
Total (without water)37,9181
Polymers37,9181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.410, 117.120, 85.740
Angle α, β, γ (deg.)90.00, 112.80, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe protein acts as a monomer.

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Components

#1: Protein
microbial transglutaminase


Mass: 37918.414 Da / Num. of mol.: 4 / Fragment: residues 1-331
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces mobaraensis (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: P81453, protein-glutamine gamma-glutamyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 550 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG1000, calcium chloride, cacodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 %(w/v)PEG10001reservoir
2100 mMcacodylate-HCl1reservoirpH5.0
325 mM1reservoirCaCl2
415 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 2, 1999
RadiationMonochromator: Si(111) (Joham type) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. all: 187008 / Num. obs: 55351 / % possible obs: 0.98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.38 % / Biso Wilson estimate: 26.25 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.13 / % possible all: 0.921
Reflection
*PLUS
% possible obs: 0.98 % / Num. measured all: 187008 / Rmerge(I) obs: 0.04
Reflection shell
*PLUS
% possible obs: 92.1 % / Rmerge(I) obs: 0.13

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
X-PLOR3.1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.4→40 Å / σ(F): 2
Stereochemistry target values: standard set of QUANTA release98 (MSI)
RfactorNum. reflection% reflectionSelection details
Rfree0.2662 2752 -random
Rwork0.1991 ---
all0.2046 55351 --
obs0.2026 54496 96.5 %-
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10712 0 0 550 11262
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_deg3.655
X-RAY DIFFRACTIONx_dihedral_angle_deg27.029
X-RAY DIFFRACTIONx_improper_angle_deg2.613
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS

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