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- PDB-3ipj: The crystal structure of one domain of the PTS system, IIabc comp... -

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Basic information

Entry
Database: PDB / ID: 3ipj
TitleThe crystal structure of one domain of the PTS system, IIabc component from Clostridium difficile
ComponentsPTS system, IIabc component
KeywordsTRANSFERASE / PTS system / IIabc component / PSI / Structural genomics / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / Cell membrane / Kinase / Membrane / Phosphotransferase system / Sugar transport / Transmembrane / Transport
Function / homology
Function and homology information


protein-Npi-phosphohistidine-sugar phosphotransferase / protein-N(pi)-phosphohistidine--N-acetyl-D-glucosamine phosphotransferase activity / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / membrane => GO:0016020 / metal ion binding / plasma membrane
Similarity search - Function
Glucose permease domain IIB / Phosphotransferase system, IIB component, type 1 / Phosphotransferase system, EIIC component, type 1 / Phosphotransferase system EIIB, cysteine phosphorylation site / Glucose permease domain IIB / phosphotransferase system, EIIB / PTS EIIB domains cysteine phosphorylation site signature. / PTS_EIIB type-1 domain profile. / PTS_EIIC type-1 domain profile. / Phosphotransferase system, EIIC ...Glucose permease domain IIB / Phosphotransferase system, IIB component, type 1 / Phosphotransferase system, EIIC component, type 1 / Phosphotransferase system EIIB, cysteine phosphorylation site / Glucose permease domain IIB / phosphotransferase system, EIIB / PTS EIIB domains cysteine phosphorylation site signature. / PTS_EIIB type-1 domain profile. / PTS_EIIC type-1 domain profile. / Phosphotransferase system, EIIC / Phosphotransferase system, EIIC / Phosphotransferase system, sugar-specific permease EIIA type 1 / phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1 / PTS_EIIA type-1 domain profile. / Duplicated hybrid motif / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS system, sucrose-specific IIABC component
Similarity search - Component
Biological speciesClostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsZhang, R. / Bigelow, L. / Cobb, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of one domain of the PTS system, IIabc component from Clostridium difficile
Authors: Zhang, R. / Bigelow, L. / Cobb, G. / Joachimiak, A.
History
DepositionAug 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: PTS system, IIabc component
B: PTS system, IIabc component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,7044
Polymers21,5732
Non-polymers1312
Water4,630257
1
A: PTS system, IIabc component


Theoretical massNumber of molelcules
Total (without water)10,7871
Polymers10,7871
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PTS system, IIabc component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9173
Polymers10,7871
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.635, 34.734, 72.195
Angle α, β, γ (deg.)90.00, 90.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PTS system, IIabc component


Mass: 10786.523 Da / Num. of mol.: 2 / Fragment: sequence database residues 2-93
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium difficile (bacteria) / Strain: 630 / Gene: CD0469, GI:115249482 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q188R0
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.005M Cobalt Chloride, 0.05M Nickel Chloride, 0.05M Cadmium Chloride, 0.05M Magnesium Chloride, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 6, 2009 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.496
ReflectionResolution: 1.2→37.635 Å / Num. all: 58676 / Num. obs: 52533 / % possible obs: 89.53 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 19.8
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 2.17 / % possible all: 45.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
CNSrefinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→37.635 Å / σ(F): 1.34 / Phase error: 18.86 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1699 2791 5.31 %
Rwork0.1334 --
obs0.1352 52533 89.53 %
all-58676 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.696 Å2 / ksol: 0.34 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.2501 Å2-0 Å20.9217 Å2
2--1.9165 Å20 Å2
3----2.1995 Å2
Refinement stepCycle: LAST / Resolution: 1.2→37.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 2 257 1767
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0241510
X-RAY DIFFRACTIONf_angle_d1.9092008
X-RAY DIFFRACTIONf_dihedral_angle_d16.211580
X-RAY DIFFRACTIONf_chiral_restr0.114238
X-RAY DIFFRACTIONf_plane_restr0.006250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2-1.22070.2821590.27671264X-RAY DIFFRACTION98
1.2207-1.24290.2559620.24981501X-RAY DIFFRACTION98
1.2429-1.26690.2571810.23741732X-RAY DIFFRACTION98
1.2669-1.29270.24531130.22621956X-RAY DIFFRACTION98
1.2927-1.32080.24741200.21882321X-RAY DIFFRACTION98
1.3208-1.35150.20881500.20492573X-RAY DIFFRACTION98
1.3515-1.38530.21341540.19372725X-RAY DIFFRACTION98
1.3853-1.42280.19481390.18122677X-RAY DIFFRACTION98
1.4228-1.46470.20131370.18992695X-RAY DIFFRACTION98
1.4647-1.5120.18381400.17022749X-RAY DIFFRACTION98
1.512-1.5660.19631480.16292714X-RAY DIFFRACTION98
1.566-1.62870.18021570.15992714X-RAY DIFFRACTION98
1.6287-1.70280.18181350.16362746X-RAY DIFFRACTION98
1.7028-1.79260.18171550.15462748X-RAY DIFFRACTION98
1.7926-1.90490.19511490.14482768X-RAY DIFFRACTION98
1.9049-2.0520.18571420.13432801X-RAY DIFFRACTION98
2.052-2.25840.15151630.10932757X-RAY DIFFRACTION98
2.2584-2.58520.14531640.10642790X-RAY DIFFRACTION98
2.5852-3.25680.16681430.10132836X-RAY DIFFRACTION98
3.2568-37.65350.12121470.08792808X-RAY DIFFRACTION98

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