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- PDB-3e8v: Crystal structure of a possible transglutaminase-family protein p... -

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Basic information

Entry
Database: PDB / ID: 3e8v
TitleCrystal structure of a possible transglutaminase-family protein proteolytic fragment from Bacteroides fragilis
ComponentsPossible transglutaminase-family protein
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Carboxypeptidase-like, regulatory domain / Transglutaminase-like superfamily / Transglutaminase/protease-like homologues / Transglutaminase-like / Papain-like cysteine peptidase superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Unknown ligand / Possible transglutaminase-family protein
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsBonanno, J.B. / Rutter, M. / Bain, K.T. / Hu, S. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a possible transglutaminase-family protein proteolytic fragment from Bacteroides fragilis
Authors: Bonanno, J.B. / Rutter, M. / Bain, K.T. / Hu, S. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionAug 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 21, 2024Group: 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

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Assembly

Deposited unit
A: Possible transglutaminase-family protein


Theoretical massNumber of molelcules
Total (without water)8,9182
Polymers8,9181
Non-polymers01
Water905
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.006, 82.006, 32.367
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-1-

UNL

Detailsauthors state that the biological unit is probable dimer mediated by unknown ion.

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Components

#1: Protein Possible transglutaminase-family protein


Mass: 8917.956 Da / Num. of mol.: 1 / Fragment: residues 289-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Strain: ATCC 25285 / Gene: BF1045 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LGG0
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE CRYSTAL IS FORMED FROM A FRAGMENT OF A PROTEIN OF 847 AMINO ACIDS, AND IT IS ...AUTHORS STATE THAT THE CRYSTAL IS FORMED FROM A FRAGMENT OF A PROTEIN OF 847 AMINO ACIDS, AND IT IS UNKNOWN WHAT THE ACTUAL TERMINI ARE FOR THE CRYSTALLIZED FRAGMENT. THE WHOLE SEQUENCE OF 847 RESIDUES IS SLGELFAVFNEKLTIPEQEALMFLYAYMPTGDVTDYTGDYYLENVRLSDQARREMPWGKE IPDDVFRHFVLPIRVNNENLDDSRRVFYNELKDRVKNLSLHDAVLEVNHWCHEKVIYTPS DARTSAPLASVKTAYGRCGEESTFTVAALRSVGIPARQVYTPRWAHTDDNHAWVEAWVDG KWYFFGACEPEPVLNLGWFNAPASRGMLMHTKVFGRYTGQEEIMYETPNYTEINVIDNYA PTAKGSVLVTDAEGQPVADATVEFKVYNYAEFYTVATKHTDRSGHASLTAGKGDMLVWAS KDGRFGYSKLSFGKDNELKITLDKNASETYSLPLDIVPPAEGANLPEVTPEQRTENDRRM AQEDSIRNAYVATFITEEQARTFAKENKLDETETVRLLIASRGNHQTLTDFLSDAVKADK AGQAISLLKVVSAKDLRDVSPEVLNDHLNNSGLPASEDFCSNVLNPRVANEMITPYKAFF RKEIPASEAEAFRKNPQALVEWCKKEITINNELNSQRIPMSPMGVWKARVADEKSRNIFF VSMARSLGIPAWIDEVTGKIQYRTFNDNNLKNGKVYDVDFEAAQQTQAPTGTLVARYRPI PSLSDPKYYSHFTLSKFRNGTFQLLNYDEGDVDMGGGATWSNLLKNGARLDTGYYMMVTG TRMASGAVLANVTFFTIEEGKTTTVDLVMRESKDQVQVIGNFNSESTYLPIGTSEPQSIL QTCGRGYYVVAVLGAGQEPTNHALRDIAALSGEFEKWGRKMVLLFPSEEQYKKFRPSEFP GLPSTITYGIDVDGAIQKQIAESMKLPNSTILPMFIIGDTFNRVVFVSQGYTIGLGEQLM KVIHGEG

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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: 3.52 Å3/Da / Density % sol: 65.09 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 100mM sodium cacodylate pH 6.5, 1.4M sodium acetate hydrate, Vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 18, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.4→19.699 Å / Num. all: 5084 / Num. obs: 5079 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 22 % / Biso Wilson estimate: 51.6 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 30.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 22.3 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 5.8 / Num. measured all: 16470 / Num. unique all: 737 / Rsym value: 0.574 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
SCALA3.2.19data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.4→15 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.924 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.22 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.82 / SU B: 6.792 / SU ML: 0.155 / SU R Cruickshank DPI: 0.276 / SU Rfree: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.276 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; UNKNOWN ION MODELED AS BA; PROTEOLYTIC FRAGMENT IDENTIFIED BY SEQUENCE REGISTER
RfactorNum. reflection% reflectionSelection details
Rfree0.243 224 4.4 %RANDOM
Rwork0.225 ---
obs0.226 5050 99.92 %-
all-5054 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 57.06 Å2 / Biso mean: 36.837 Å2 / Biso min: 18.71 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å2-0.54 Å20 Å2
2---1.07 Å20 Å2
3---1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms600 0 1 5 606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022612
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.939830
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.364581
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68725.21723
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.7731591
X-RAY DIFFRACTIONr_chiral_restr0.090.295
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02458
X-RAY DIFFRACTIONr_nbd_refined0.2410.2217
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2410
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.227
X-RAY DIFFRACTIONr_metal_ion_refined0.3250.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4360.221
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.21
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.320.23
X-RAY DIFFRACTIONr_mcbond_it0.9241.5402
X-RAY DIFFRACTIONr_mcangle_it1.7082631
X-RAY DIFFRACTIONr_scbond_it2.0163215
X-RAY DIFFRACTIONr_scangle_it3.1224.5199
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 11 -
Rwork0.349 353 -
all-364 -
obs-353 100 %

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