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- PDB-4mxm: Crystal structure of superantigen pfit -

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Basic information

Entry
Database: PDB / ID: 4mxm
TitleCrystal structure of superantigen pfit
ComponentsTranscriptional regulator I2
KeywordsDNA BINDING PROTEIN / Superantigen
Function / homologyTetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsLiu, L.H. / Chen, H. / Li, H.M.
CitationJournal: Plos Pathog. / Year: 2013
Title: Pfit is a structurally novel Crohn's disease-associated superantigen.
Authors: Liu, L. / Chen, H. / Brecher, M.B. / Li, Z. / Wei, B. / Nandi, B. / Zhang, J. / Ling, H. / Winslow, G. / Braun, J. / Li, H.
History
DepositionSep 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator I2
B: Transcriptional regulator I2


Theoretical massNumber of molelcules
Total (without water)45,9062
Polymers45,9062
Non-polymers00
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-18 kcal/mol
Surface area19320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.186, 110.998, 62.075
Angle α, β, γ (deg.)90.00, 100.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transcriptional regulator I2


Mass: 22953.010 Da / Num. of mol.: 2 / Fragment: transcriptional regulator I2: unp residues 10-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: A506 / Gene: I2, pfiT, PflA506_3695 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I2BPL4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.75 Å3/Da / Density % sol: 55.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 4-8% PEG 3350, 0.1 M Tris, 0.2 M ammonium acetate, 5 mM MgCl2, 5 mM DTT, 5% isopropanol, and 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97905 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 11, 2005 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97905 Å / Relative weight: 1
ReflectionResolution: 1.95→45.7 Å / Num. all: 35150 / Num. obs: 35150 / % possible obs: 97.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 30.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.694 / Mean I/σ(I) obs: 2.5 / Rsym value: 0.694 / % possible all: 97.1

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.95→29.212 Å / SU ML: 0.31 / σ(F): 1.34 / Phase error: 28.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2691 1701 5.01 %
Rwork0.2464 --
obs0.2475 33759 93.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.594 Å2 / ksol: 0.371 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.7946 Å20 Å2-1.915 Å2
2--6.3205 Å2-0 Å2
3---0.4741 Å2
Refinement stepCycle: LAST / Resolution: 1.95→29.212 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2954 0 0 213 3167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023001
X-RAY DIFFRACTIONf_angle_d0.5474043
X-RAY DIFFRACTIONf_dihedral_angle_d14.0291097
X-RAY DIFFRACTIONf_chiral_restr0.041464
X-RAY DIFFRACTIONf_plane_restr0.001510
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9463-2.01590.37293230.3486161X-RAY DIFFRACTION91
2.0159-2.09660.31833290.29626309X-RAY DIFFRACTION93
2.0966-2.1920.31653330.27716354X-RAY DIFFRACTION93
2.192-2.30750.3033340.26976395X-RAY DIFFRACTION94
2.3075-2.4520.29383440.25246337X-RAY DIFFRACTION94
2.452-2.64120.28073410.24646475X-RAY DIFFRACTION95
2.6412-2.90680.28663400.23796530X-RAY DIFFRACTION96
2.9068-3.32690.2613550.23346659X-RAY DIFFRACTION97
3.3269-4.18950.23023440.226493X-RAY DIFFRACTION95
4.1895-29.21540.25923270.25166173X-RAY DIFFRACTION91

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