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- PDB-3iu0: Structural basis for zymogen activation and substrate binding of ... -

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Basic information

Entry
Database: PDB / ID: 3iu0
TitleStructural basis for zymogen activation and substrate binding of transglutaminase from Streptomyces mobaraense
ComponentsProtein-glutamine gamma-glutamyltransferaseTransglutaminase
KeywordsTRANSFERASE / MTGase / zymogen / pro-enzyme / cross-linking / Acyltransferase
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLi, T.T.
CitationJournal: To be Published
Title: Structural basis for zymogen activation and substrate binding of transglutaminase from Streptomyces mobaraense
Authors: Yang, M. / Wang, J.M. / Wu, T.K. / Li, T.T.
History
DepositionAug 28, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein-glutamine gamma-glutamyltransferase


Theoretical massNumber of molelcules
Total (without water)43,3331
Polymers43,3331
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.333, 67.123, 83.969
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 43333.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces mobaraensis (bacteria) / Plasmid: pET21d / 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.: 150 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 30% PEG8000, 50mM NaCl, 1mM EDTA, 1mM beta-mercaptoethanol, 0.01% NaN3, 100mM cacodylic acid, pH5.0 and 2% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
RadiationMonochromator: blue-optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 29327 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.2 % / Biso Wilson estimate: 27.7 Å2 / Rmerge(I) obs: 0.043 / Net I/σ(I): 39.2
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 8 % / Rmerge(I) obs: 0.238 / Mean I/σ(I) obs: 8.1 / Num. unique all: 3592 / Rsym value: 0.238 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IU4

1iu4


Resolution: 1.9→19.129 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.244 / WRfactor Rwork: 0.21 / SU B: 3.246 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.185 / ESU R Free: 0.16
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.24394 2953 10.088 %RANDOM
Rwork0.20971 26318 --
all0.213 ---
obs0.21319 26318 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.615 Å2
Baniso -1Baniso -2Baniso -3
1-0.015 Å20 Å20 Å2
2--0.004 Å20 Å2
3----0.019 Å2
Refine analyzeLuzzati coordinate error obs: 0.278 Å / Luzzati d res low obs: 6 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2777 0 0 150 2927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212855
X-RAY DIFFRACTIONr_angle_refined_deg1.0561.9223879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1425352
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.94723.462156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.27815413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.941526
X-RAY DIFFRACTIONr_chiral_restr0.0790.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212328
X-RAY DIFFRACTIONr_nbd_refined0.1830.21252
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21940
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0940.2193
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.211
X-RAY DIFFRACTIONr_mcbond_it0.5421.51763
X-RAY DIFFRACTIONr_mcangle_it1.01722802
X-RAY DIFFRACTIONr_scbond_it1.55431092
X-RAY DIFFRACTIONr_scangle_it2.5794.51077
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)WRfactor Rwork
1.9-1.9490.272140.21218910.218210799.9050.212
1.949-2.0020.2742110.20618410.21320521000.206
2.002-2.0590.2831960.2118180.21720141000.21
2.059-2.1220.2731920.21417540.2219461000.214
2.122-2.190.2821940.21116950.21818891000.211
2.19-2.2660.2381660.21416790.21618451000.214
2.266-2.350.2781880.21615800.22317681000.216
2.35-2.4450.2361770.21815370.2217141000.218
2.445-2.5520.3121790.22714730.23616521000.227
2.552-2.6740.2611500.23514260.23715761000.235
2.674-2.8150.2671460.23713590.23915051000.237
2.815-2.9820.3121330.22412920.23214251000.224
2.982-3.1830.2631490.22511980.22913471000.225
3.183-3.430.2431320.21411300.21712621000.214
3.43-3.7450.2191280.19410560.19611841000.194
3.745-4.1670.1861020.1689760.1710781000.168
4.167-4.7740.168990.188500.17995099.8950.18
4.774-5.7580.24870.2097420.2128291000.209
5.758-7.7980.226700.2316100.236801000.231
7.798-19.1290.232400.2154110.2164511000.215

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