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- PDB-4pa5: Tgl - a bacterial spore coat transglutaminase - cystamine complex -

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Basic information

Entry
Database: PDB / ID: 4pa5
TitleTgl - a bacterial spore coat transglutaminase - cystamine complex
ComponentsProtein-glutamine gamma-glutamyltransferase
KeywordsTRANSFERASE / protein cross-linking / baterial spore coat / NlpC/P60 endopeptidase / 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 / 2-AMINO-ETHANETHIOL / CITRATE ANION / TRIETHYLENE GLYCOL / Protein-glutamine gamma-glutamyltransferase
Function and homology information
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.86 Å
AuthorsBrito, J.A. / Placido, D. / Fernandes, C.G. / Lousa, D. / Isidro, A. / Soares, C.M. / Pohl, J. / Carrondo, M.A. / Henriques, A.O. / Archer, M.
Funding support Portugal, 3items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPOCI/BIA-BCM/60855/2004 Portugal
Fundacao para a Ciencia e a TecnologiaPOCTI/BCI/48647/2002 Portugal
Fundacao para a Ciencia 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
DepositionApr 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
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
Revision 2.0May 1, 2024Group: Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_nonpoly_scheme ...atom_site / pdbx_nonpoly_scheme / struct_conn / struct_conn_type / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.occupancy / _pdbx_nonpoly_scheme.auth_seq_num / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.id / _struct_site_gen.auth_seq_id

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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)61,31412
Polymers60,1412
Non-polymers1,17310
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-52 kcal/mol
Surface area21840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.350, 98.350, 65.814
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 / 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 , 9 types, 214 molecules

#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-DHL / 2-AMINO-ETHANETHIOL / 2,3-DESHYDROLANTHIONINE


Type: L-peptide linking / Mass: 77.149 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7NS
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#9: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.81 Å3/Da / Density % sol: 56.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4
Details: 41% (w/V) PEG 400 0.1 M sodium citrate pH 4.0 0.2 M lithium sulfate
PH range: 4.0-5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.86→36.57 Å / Num. obs: 47409 / % possible obs: 84.8 % / Redundancy: 4.1 % / Net I/σ(I): 12.1

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Processing

Software
NameVersionClassification
XDS31-12-2013data scaling
SHARP2.8.2phasing
BUSTER-TNT2.1refinement
PHENIX1.8.4-dev1565refinement
RefinementMethod to determine structure: MIR / Resolution: 1.86→36.57 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.213 --
Rwork0.167 --
obs-47409 84.8 %
Refinement stepCycle: LAST / Resolution: 1.86→36.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 71 204 4227
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)
17.8026-0.46163.52988.54762.95492.96390.3293-1.466-2.31541.536-0.0281.30551.3841-0.4226-0.22251.0614-0.1758-0.08390.77390.32191.375729.39554.267564.4733
22.2926-0.10821.96532.5248-1.56315.13780.1401-1.069-1.54910.8370.31910.84060.6012-0.4422-0.42950.6175-0.01210.01040.67530.27340.900526.433311.116961.5064
32.83240.4582-0.79542.7889-0.46752.01660.0564-0.2613-0.04190.275-0.0593-0.3185-0.0598-0.04760.00640.1915-0.0001-0.07970.23650.03260.229536.436630.095950.3548
46.0698-1.83430.95924.24840.51240.66330.07110.29210.48140.09650.0720.3725-0.2332-0.453-0.17220.26490.04190.09630.53540.12450.321415.328735.059350.7175
56.3095-1.3669-3.07285.69832.34437.616-0.0746-0.4214-0.65770.35620.2285-1.20790.7440.7633-0.13530.3157-0.019-0.09980.27660.05860.551235.054414.50249.6144
65.156-2.38341.20012.3308-1.51133.0361-0.58970.5133-0.6851-1.19340.58071.40211.8626-1.3244-0.04130.9872-0.2893-0.17480.58630.07760.821918.1791-0.828831.2697
72.7151-1.30162.90994.8041-0.18643.5144-0.090.2738-0.1929-1.46180.35850.30060.2834-0.3138-0.42270.7703-0.0846-0.04860.31980.02050.439225.85952.123531.2669
82.50631.4619-0.57234.9501-0.71371.4293-0.22080.1432-0.0485-0.69110.1477-0.00430.2806-0.09910.05990.31680.0052-0.04290.2062-0.00130.243235.504623.878128.5759
95.0887-1.2448-0.00780.9093-1.26972.8403-0.0115-0.16760.0564-0.53320.3301-1.39530.16110.502-0.24830.58830.00730.24920.3345-0.16231.051349.808712.649530.2487
103.23781.8048-1.2911.5093-0.16091.1925-0.0545-0.589-0.118-0.30830.1229-1.69270.43290.8803-0.03050.53590.20950.2630.556-0.19921.600957.22267.636232.4307
116.557-2.17730.62762.0988-0.13516.65060.3265-0.45870.2942-0.28730.13820.1240.1583-1.0953-0.38970.3648-0.07630.00230.38880.05960.469226.091216.036837.088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 20 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 41 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 168 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 169 through 230 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 231 through 245 )A0
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 20 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 21 through 41 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 42 through 168 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 169 through 206 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 207 through 230 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 231 through 245 )B0

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