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- PDB-4mo7: Crystal structure of superantigen PfiT -

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Basic information

Entry
Database: PDB / ID: 4mo7
TitleCrystal structure of superantigen PfiT
ComponentsTranscriptional regulator I2
KeywordsTRANSCRIPTION / TetR / Superantigen
Function / homologyTetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / BETA-MERCAPTOETHANOL / :
Function and homology information
Biological speciesPseudomonas fluorescens A506 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.701 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 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: 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 / struct_site
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 / _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: Transcriptional regulator I2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7403
Polymers23,6371
Non-polymers1022
Water2,000111
1
A: Transcriptional regulator I2
hetero molecules

A: Transcriptional regulator I2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,4796
Polymers47,2742
Non-polymers2054
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_857-x+3,y,-z+21
Buried area2390 Å2
ΔGint-18 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.226, 93.661, 53.557
Angle α, β, γ (deg.)90.00, 109.82, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

MG

21A-357-

HOH

31A-384-

HOH

41A-388-

HOH

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Components

#1: Protein Transcriptional regulator I2


Mass: 23637.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens A506 (bacteria)
Gene: pfiT, PflA506_3695 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: I2BPL4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 1.86 Å3/Da / Density % sol: 33.8 %
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: 1.04023 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 11, 2005
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04023 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 57293 / Num. obs: 18843 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3 % / Rmerge(I) obs: 0.049 / Rsym value: 0.049 / Net I/σ(I): 30.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.556 / Mean I/σ(I) obs: 2.7 / Num. unique all: 1851 / Rsym value: 0.556 / % possible all: 98.8

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIX(phenix.refine: 1.7.3_928)model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7.3_928phasing
RefinementMethod to determine structure: SAD / Resolution: 1.701→25.192 Å / SU ML: 0.27 / σ(F): 1.35 / Phase error: 24.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 938 4.98 %RANDOM
Rwork0.1886 ---
obs0.1908 18840 99.32 %-
all-18840 --
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.804 Å2 / ksol: 0.404 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.3004 Å20 Å2-1.3445 Å2
2---0.3717 Å2-0 Å2
3---1.6721 Å2
Refinement stepCycle: LAST / Resolution: 1.701→25.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1482 0 5 111 1598
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161568
X-RAY DIFFRACTIONf_angle_d1.5722121
X-RAY DIFFRACTIONf_dihedral_angle_d15.408581
X-RAY DIFFRACTIONf_chiral_restr0.105239
X-RAY DIFFRACTIONf_plane_restr0.006273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7006-1.79020.38511340.30542505X-RAY DIFFRACTION97
1.7902-1.90240.34421300.24412545X-RAY DIFFRACTION100
1.9024-2.04920.2451370.20842559X-RAY DIFFRACTION100
2.0492-2.25530.23671300.18112565X-RAY DIFFRACTION100
2.2553-2.58130.23041380.17052558X-RAY DIFFRACTION100
2.5813-3.25110.2071380.17312580X-RAY DIFFRACTION100
3.2511-25.19430.2141310.18062590X-RAY DIFFRACTION99

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