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- PDB-4xz7: Crystal structure of a TGase -

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Basic information

Entry
Database: PDB / ID: 4xz7
TitleCrystal structure of a TGase
ComponentsPutative uncharacterized protein
KeywordsTRANSFERASE / TGase acitivy / homodimer / anti-phacocytosis / virulence factor
Function / homologyTransglutaminase-like superfamily / Transglutaminase-like / Papain-like cysteine peptidase superfamily / Transglutaminase-like domain-containing protein
Function and homology information
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.101 Å
AuthorsYu, J. / Ge, J. / Yang, M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Functional and Structural Characterization of the Antiphagocytic Properties of a Novel Transglutaminase from Streptococcus suis
Authors: Yu, J. / Pian, Y. / Ge, J. / Guo, J. / Zheng, Y. / Jiang, H. / Hao, H. / Yuan, Y. / Jiang, Y. / Yang, M.
History
DepositionFeb 4, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)91,4742
Polymers91,4742
Non-polymers00
Water8,413467
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-41 kcal/mol
Surface area35970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.133, 91.935, 102.172
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 Putative uncharacterized protein / TGase


Mass: 45737.020 Da / Num. of mol.: 2 / Fragment: UNP residues 39-437
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A5JSJ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 467 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.2 / Details: 0.1M Hepes, 0.2M NaCl, 20%(w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 49556 / % possible obs: 100 % / Redundancy: 10.2 % / Rsym value: 0.091 / Net I/σ(I): 26.95
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 3.25 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.101→45.967 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2361 2417 5.09 %
Rwork0.192 --
obs0.1943 47481 95.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.101→45.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6048 0 0 467 6515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086172
X-RAY DIFFRACTIONf_angle_d1.0538340
X-RAY DIFFRACTIONf_dihedral_angle_d15.3432236
X-RAY DIFFRACTIONf_chiral_restr0.043902
X-RAY DIFFRACTIONf_plane_restr0.0041084
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1014-2.14430.2762850.22981892X-RAY DIFFRACTION69
2.1443-2.1910.31341220.24222149X-RAY DIFFRACTION79
2.191-2.24190.27961380.23382370X-RAY DIFFRACTION87
2.2419-2.2980.29421150.23522606X-RAY DIFFRACTION95
2.298-2.36010.28251400.23412696X-RAY DIFFRACTION99
2.3601-2.42960.28431370.232742X-RAY DIFFRACTION100
2.4296-2.5080.25041330.21642770X-RAY DIFFRACTION100
2.508-2.59760.27931580.21662724X-RAY DIFFRACTION100
2.5976-2.70160.27421770.21392727X-RAY DIFFRACTION100
2.7016-2.82450.26041430.21332735X-RAY DIFFRACTION100
2.8245-2.97340.24061410.20882784X-RAY DIFFRACTION100
2.9734-3.15970.27021520.20912744X-RAY DIFFRACTION100
3.1597-3.40360.22441500.19012793X-RAY DIFFRACTION100
3.4036-3.74590.241410.1752769X-RAY DIFFRACTION100
3.7459-4.28760.18921700.15712791X-RAY DIFFRACTION100
4.2876-5.40060.18081390.15142849X-RAY DIFFRACTION100
5.4006-45.97850.20371760.16942923X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 19.0173 Å / Origin y: -15.6556 Å / Origin z: 20.3542 Å
111213212223313233
T0.1944 Å20.0137 Å20.0188 Å2-0.224 Å20.0662 Å2--0.1232 Å2
L0.9106 °20.3958 °20.2687 °2-0.765 °2-0.0257 °2--0.5918 °2
S0.0532 Å °-0.2221 Å °-0.0505 Å °0.1139 Å °-0.1067 Å °-0.1377 Å °-0.009 Å °-0.0119 Å °0.0579 Å °
Refinement TLS groupSelection details: all

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