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- PDB-5i45: 1.35 Angstrom Crystal Structure of C-terminal Domain of Glycosyl ... -

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Basic information

Entry
Database: PDB / ID: 5i45
Title1.35 Angstrom Crystal Structure of C-terminal Domain of Glycosyl Transferase Group 1 Family Protein (LpcC) from Francisella tularensis.
ComponentsGlycosyl transferases group 1 family protein
KeywordsTRANSFERASE / Glycosyl Transferase Group 1 Family / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


Transferases / glycosyltransferase activity
Similarity search - Function
Glycosyl transferases group 1 / Glycosyl transferase, family 1 / Glycosyl transferases group 1 / Glycogen Phosphorylase B; / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glycosyl transferases group 1 family protein
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsMinasov, G. / Filippova, E. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.35 Angstrom Crystal Structure of C-terminal Domain of Glycosyl Transferase Group 1 Family Protein (LpcC) from Francisella tularensis.
Authors: Minasov, G. / Filippova, E. / Shuvalova, L. / Kiryukhina, O. / Dubrovska, I. / Shatsman, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionFeb 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl transferases group 1 family protein


Theoretical massNumber of molelcules
Total (without water)24,6251
Polymers24,6251
Non-polymers00
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.484, 58.962, 41.646
Angle α, β, γ (deg.)90.00, 117.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Glycosyl transferases group 1 family protein


Mass: 24624.842 Da / Num. of mol.: 1 / Fragment: unp residues 140-354
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: lpcC, FTT_1235c, BZ14_1572 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) magic / References: UniProt: Q5NFJ9, Transferases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 1.73 Å3/Da / Density % sol: 29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Protein: 10.4 mg/ml, 0.01M Tris-HCL (pH 8.3); Screen: PACT (D6), 0.1M MMT buffer (pH 9.0), 25% (w/v) PEG 1500.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 8, 2016 / Details: C(111)
RadiationMonochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. obs: 36249 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 15.5 Å2 / CC1/2: 0.811 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 35.5
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.6 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB-3C4Q

3c4q


Resolution: 1.35→29.55 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.084 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.069 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20303 1654 4.6 %RANDOM
Rwork0.16157 ---
obs0.16355 34441 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.506 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å20 Å2-0.27 Å2
2---0.95 Å20 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.35→29.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1544 0 0 269 1813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191886
X-RAY DIFFRACTIONr_bond_other_d0.0020.021817
X-RAY DIFFRACTIONr_angle_refined_deg1.561.9712585
X-RAY DIFFRACTIONr_angle_other_deg0.90134228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4865254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36325.46586
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.56715344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.774159
X-RAY DIFFRACTIONr_chiral_restr0.10.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0230.0212261
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02418
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7170.934941
X-RAY DIFFRACTIONr_mcbond_other0.710.933940
X-RAY DIFFRACTIONr_mcangle_it1.1871.3981220
X-RAY DIFFRACTIONr_mcangle_other1.1861.3991221
X-RAY DIFFRACTIONr_scbond_it1.041.085945
X-RAY DIFFRACTIONr_scbond_other1.0391.086946
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.6341.5771366
X-RAY DIFFRACTIONr_long_range_B_refined5.4859.5332495
X-RAY DIFFRACTIONr_long_range_B_other5.2428.4692340
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 113 -
Rwork0.25 2533 -
obs--99.21 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2605-1.33490.15311.77930.08220.83950.01310.1279-0.1493-0.0531-0.06240.08890.1126-0.09570.04920.0546-0.0279-0.00220.0906-0.00550.011310.84524.952618.7759
21.07030.28740.09031.535-0.57231.1277-0.01620.01250.05020.03530.0090.0601-0.0107-0.09280.00720.00230.00470.00280.0801-0.00170.01329.209430.622235.5842
30.8107-1.67790.80896.9283-2.04641.8155-0.0511-0.0285-0.10660.25180.12620.2595-0.048-0.2599-0.07510.01140.00590.01120.08380.00350.01862.69124.75543.7605
40.6861-0.05560.10820.775-0.1520.9027-0.02270.0262-0.0918-0.01860.01610.01760.1412-0.11270.00660.0269-0.02490.00630.0889-0.00540.013110.500123.125330.2938
50.8578-0.1025-0.42671.04730.0451.6685-0.0421-0.04780.00710.0425-0.0222-0.09590.06010.06830.06430.0144-0.0024-0.00650.07450.0110.014223.517828.694433.1637
62.0837-1.2883-1.0863.04271.45371.5307-0.01060.06780.08-0.02240.065-0.16690.0690.0439-0.05440.01560.00510.00130.07920.00910.013323.147432.03823.4577
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A141 - 162
2X-RAY DIFFRACTION2A163 - 203
3X-RAY DIFFRACTION3A204 - 226
4X-RAY DIFFRACTION4A227 - 260
5X-RAY DIFFRACTION5A261 - 305
6X-RAY DIFFRACTION6A306 - 335

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