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- PDB-3tw5: Crystal structure of the GP42 transglutaminase from Phytophthora sojae -

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Basic information

Entry
Database: PDB / ID: 3tw5
TitleCrystal structure of the GP42 transglutaminase from Phytophthora sojae
ComponentsTransglutaminase elicitor
KeywordsTRANSFERASE / Cysteine protease / Convergent evolution / Innate immunity / Pathogen-associated molecular pattern (PAMP) / Phytophthora / tranglutaminase
Function / homology
Function and homology information


protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity
Similarity search - Function
Transglutaminase elicitor, body domain / Transglutaminase elicitor / Transglutaminase elicitor / Herpes Virus-1 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Glycoprotein elicitor / Glycoprotein elicitor
Similarity search - Component
Biological speciesPhytophthora sojae (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.95 Å
AuthorsReiss, K. / Kirchner, E. / Zocher, G. / Stehle, T.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural and Phylogenetic Analyses of the GP42 Transglutaminase from Phytophthora sojae Reveal an Evolutionary Relationship between Oomycetes and Marine Vibrio Bacteria.
Authors: Reiss, K. / Kirchner, E. / Gijzen, M. / Zocher, G. / Loffelhardt, B. / Nurnberger, T. / Stehle, T. / Brunner, F.
History
DepositionSep 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Dec 21, 2011Group: Database references
Revision 1.3Oct 21, 2020Group: Data collection / Database references / Derived calculations
Category: reflns_shell / struct_ref_seq_dif / struct_site
Item: _reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all ..._reflns_shell.Rmerge_I_obs / _reflns_shell.number_unique_all / _reflns_shell.pdbx_Rsym_value / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transglutaminase elicitor
B: Transglutaminase elicitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,8924
Polymers80,4492
Non-polymers4432
Water00
1
A: Transglutaminase elicitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,6673
Polymers40,2251
Non-polymers4432
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transglutaminase elicitor


Theoretical massNumber of molelcules
Total (without water)40,2251
Polymers40,2251
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)195.480, 195.480, 137.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A163 - 528
2114B163 - 528

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Components

#1: Protein Transglutaminase elicitor


Mass: 40224.648 Da / Num. of mol.: 2 / Fragment: transglutaminase domain / Mutation: C290S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phytophthora sojae (eukaryote) / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / Strain (production host): GS115
References: UniProt: Q6Q475, UniProt: Q01928*PLUS, protein-glutamine gamma-glutamyltransferase
#2: Chemical ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 4.71 Å3/Da / Density % sol: 73.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 11
Details: 1.6M ammonium sulfate, 0.2M lithium sulfate, 0.1M N-cyclohexyl-3-aminopropanesulfonic acid (CAPS), pH 11.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06DA11
SYNCHROTRONSLS X06DA21.255
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDJun 28, 2010
MARMOSAIC 225 mm CCD2CCDFeb 25, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111)SINGLE WAVELENGTHMx-ray1
2SI(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.2551
ReflectionResolution: 2.95→30 Å / Num. all: 33060 / Num. obs: 31882 / % possible obs: 96.4 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.09 / Net I/σ(I): 15.5
Reflection shellResolution: 2.95→3.026 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.75 / Rsym value: 0.583 / % possible all: 98.2

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Processing

Software
NameVersionClassification
XDSdata scaling
SHARPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: SIRAS / Resolution: 2.95→30 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.899 / SU B: 12.137 / SU ML: 0.221 / Cross valid method: THROUGHOUT / σ(F): -3 / ESU R Free: 0.296 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23426 1594 5 %RANDOM
Rwork0.21488 ---
obs0.21584 30288 96.59 %-
all-31882 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.922 Å2
Baniso -1Baniso -2Baniso -3
1--1.75 Å2-0.87 Å20 Å2
2---1.75 Å20 Å2
3---2.62 Å2
Refinement stepCycle: LAST / Resolution: 2.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5227 0 28 0 5255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225403
X-RAY DIFFRACTIONr_angle_refined_deg0.8891.9437383
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4615684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28125.179224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.37715783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.963158
X-RAY DIFFRACTIONr_chiral_restr0.060.2808
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214140
X-RAY DIFFRACTIONr_mcbond_it0.34123412
X-RAY DIFFRACTIONr_mcangle_it0.61625463
X-RAY DIFFRACTIONr_scbond_it0.30431991
X-RAY DIFFRACTIONr_scangle_it0.52931920
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2604 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.240.5
Bmedium thermal0.122
LS refinement shellResolution: 2.95→3.026 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 121 -
Rwork0.294 2220 -
obs-8502 98.16 %

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