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- PDB-4p8i: Tgl - a bacterial spore coat transglutaminase -

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Basic information

Entry
Database: PDB / ID: 4p8i
TitleTgl - a bacterial spore coat transglutaminase
ComponentsProtein-glutamine gamma-glutamyltransferaseTransglutaminase
KeywordsTRANSFERASE / protein cross-linking / bacterial spore coat / NlpC/P60 endopeptidases / papain
Function / homologyProtein-glutamine gamma-glutamyltransferase / Protein-glutamine gamma-glutamyltransferase, bacteria / protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / sporulation resulting in formation of a cellular spore / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Protein-glutamine gamma-glutamyltransferase
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsBrito, J.A. / Placido, D. / Fernandes, C. / Lousa, D. / Isidro, A. / Soares, C.M. / Pohl, J. / Carrondo, M.A. / Henriques, A.O. / Archer, M.
Funding support Portugal, 3items
OrganizationGrant numberCountry
Fundao para a Cincia e a TecnologiaPOCI/BIA-BCM/60855/2004 Portugal
Fundao para a Cincia e a TecnologiaPOCTI/BCI/48647/2002 Portugal
Fundao para a Cincia e a TecnologiaPTDC/SAU-NEU/103720/2008 Portugal
CitationJournal: Biochemistry / Year: 2015
Title: Structural and Functional Characterization of an Ancient Bacterial Transglutaminase Sheds Light on the Minimal Requirements for Protein Cross-Linking.
Authors: Fernandes, C.G. / Placido, D. / Lousa, D. / Brito, J.A. / Isidro, A. / Soares, C.M. / Pohl, J. / Carrondo, M.A. / Archer, M. / Henriques, A.O.
History
DepositionMar 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Structure summary
Category: citation / pdbx_struct_oper_list ...citation / pdbx_struct_oper_list / software / struct_keywords
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation ..._citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.pdbx_keywords
Revision 1.2Dec 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,8269
Polymers60,1412
Non-polymers6857
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4650 Å2
ΔGint19 kcal/mol
Surface area21720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.940, 97.940, 66.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 30070.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: tgl, yugV, yuxF, BSU31270 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P40746, protein-glutamine gamma-glutamyltransferase

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Non-polymers , 5 types, 246 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 41% (w/V) PEG 400, 0.2 M lithium sulphate, 0.1 M sodum citrate
PH range: 4-10

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.918 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.85→47.85 Å / Num. obs: 47409 / % possible obs: 88.6 % / Redundancy: 7.5 % / Net I/σ(I): 29.53

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Processing

Software
NameVersionClassification
XDS31-12-2013data scaling
SHARP2.8.2phasing
BUSTER-TNT2.1refinement
PHENIX1.8.4-dev1565refinement
RefinementResolution: 1.85→47.85 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.208 --
Rwork0.158 --
obs-47409 88.6 %
Refinement stepCycle: LAST / Resolution: 1.85→47.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 45 239 4236
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)
16.0425-2.95330.60566.2425-1.82228.04990.1822-0.8603-1.61821.04990.17770.49371.5835-0.6315-0.22190.813-0.1346-0.07650.53640.27030.678327.54448.037562.8976
22.49340.6512-0.74152.3456-0.2811.8630.0811-0.25960.0050.3032-0.0519-0.3005-0.0054-0.0384-0.01090.2108-0.0096-0.09340.23490.03860.288736.257329.930150.3389
37.2019-5.69244.37177.2255-4.78745.75120.17080.61620.70830.1569-0.1881-0.0403-0.5467-0.5360.20040.26280.05520.06920.49520.09020.295817.355335.088447.5187
44.6298-0.7053-0.93253.31070.98462.3481-0.0094-0.18580.04560.45920.00160.15370.1251-0.37780.01110.2267-0.04680.02830.34650.03750.155319.910629.018452.3785
52.4064-0.9005-0.09390.3560.10142.2394-0.47580.2659-0.2501-1.0820.40470.78451.6209-1.02560.01921.034-0.2212-0.1870.48220.05990.561118.387-0.901931.3293
69.1048-3.53650.70015.45761.36152.605-0.21890.1828-0.1862-0.75310.23060.28980.2454-0.0707-0.02060.6632-0.0722-0.11060.1994-0.02110.374925.99841.998131.3245
78.06457.1237-4.7748.3281-4.83013.959-0.47970.5988-0.013-0.96230.39750.11930.3905-0.36960.12540.5936-0.064-0.16360.2513-0.04490.327929.74313.037325.2817
85.42831.92813.27256.09240.92948.5759-0.11080.15550.227-0.74010.2457-0.3669-0.08130.3147-0.11330.245-0.01050.03880.139900.355344.886432.973127.0734
92.2225-1.3538-1.42539.22035.11073.05660.01430.30750.3853-0.9013-0.13740.7695-0.2102-0.42830.15920.4073-0.0177-0.12920.27680.07380.403232.547733.664125.1092
101.48950.8344-0.44134.11520.40381.9612-0.09180.0592-0.1065-0.37510.1992-0.18250.24090.0057-0.12330.2893-0.0183-0.05790.1948-0.01110.338337.23819.656332.1326
114.88734.81733.95256.55851.64077.0058-0.02160.11820.3815-0.17520.5071-1.4573-0.1890.9689-0.39350.5604-0.02940.15810.4332-0.24031.054751.38615.687331.7083
124.3549-0.6183-1.81881.5332-1.4012.7977-0.0737-0.2087-0.0263-0.60010.1987-1.59580.47980.7494-0.12990.63960.10510.17550.4067-0.18151.039753.01078.621129.2657
133.2397-3.9169-4.83467.75314.5377.7350.13010.3566-0.0784-0.2585-0.10120.5036-0.1101-0.8296-0.1280.3871-0.0556-0.09240.28230.0620.383726.215515.351236.6727
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 41
2X-RAY DIFFRACTION2A42 - 168
3X-RAY DIFFRACTION3A169 - 193
4X-RAY DIFFRACTION4A194 - 245
5X-RAY DIFFRACTION5B1 - 20
6X-RAY DIFFRACTION6B21 - 41
7X-RAY DIFFRACTION7B42 - 65
8X-RAY DIFFRACTION8B66 - 89
9X-RAY DIFFRACTION9B90 - 107
10X-RAY DIFFRACTION10B108 - 178
11X-RAY DIFFRACTION11B179 - 193
12X-RAY DIFFRACTION12B194 - 230
13X-RAY DIFFRACTION13B231 - 245

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