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- PDB-4amc: Crystal structure of Lactobacillus reuteri 121 N-terminally trunc... -

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Basic information

Entry
Database: PDB / ID: 4amc
TitleCrystal structure of Lactobacillus reuteri 121 N-terminally truncated glucansucrase GTFA
ComponentsGLUCANSUCRASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / REUTERANSUCRASE
Function / homology
Function and homology information


dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding
Similarity search - Function
Glucansucrase / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / KxYKxGKxW signal peptide / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Choline-binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / SH3 type barrels. / Glycosidases ...Glucansucrase / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / KxYKxGKxW signal peptide / Aspartate carbamoyltransferase regulatory subunit, C-terminal domain / Choline-binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / SH3 type barrels. / Glycosidases / Glycoside hydrolase superfamily / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesLACTOBACILLUS REUTERI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsPijning, T. / Vujicic-Zagar, A. / Kralj, S. / Dijkhuizen, L. / Dijkstra, B.W.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of the Alpha-1,6/Alpha-1,4-Specific Glucansucrase Gtfa from Lactobacillus Reuteri 121
Authors: Pijning, T. / Vujicic-Zagar, A. / Kralj, S. / Dijkhuizen, L. / Dijkstra, B.W.
History
DepositionMar 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Dec 12, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_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_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_conn.ptnr2_label_seq_id / _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: GLUCANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,0852
Polymers118,0451
Non-polymers401
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)183.871, 183.871, 374.004
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein GLUCANSUCRASE / / GLUCANSUCRASE GTFA


Mass: 118045.383 Da / Num. of mol.: 1 / Fragment: N-TERMINALLY TRUNCATED, RESIDUES 741-1781
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOBACILLUS REUTERI (bacteria) / Strain: 121 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q5SBL9, dextransucrase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

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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: 8.4 Å3/Da / Density % sol: 85 % / Description: NONE
Crystal growpH: 4.2
Details: 1 M (NH4)2SO4, 0.1 M SODIUM PHOSPHATE-CITRATE BUFFER PH 4.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 22, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.6→48.8 Å / Num. obs: 44037 / % possible obs: 100 % / Observed criterion σ(I): 2.1 / Redundancy: 8.5 % / Rmerge(I) obs: 0.22 / Net I/σ(I): 6.7
Reflection shellResolution: 3.6→3.79 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KLK

3klk


Resolution: 3.6→50 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.903 / SU B: 49.556 / SU ML: 0.324 / Cross valid method: THROUGHOUT / ESU R: 0.809 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.25972 2218 5 %RANDOM
Rwork0.23887 ---
obs0.2399 41820 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 122.986 Å2
Baniso -1Baniso -2Baniso -3
1-4.85 Å22.43 Å20 Å2
2--4.85 Å20 Å2
3----7.28 Å2
Refinement stepCycle: LAST / Resolution: 3.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8087 0 1 0 8088
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.028270
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.7631.92711241
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.08451018
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31225.501449
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.664151316
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1761532
X-RAY DIFFRACTIONr_chiral_restr0.0540.21194
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0216533
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.6→3.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 150 -
Rwork0.332 2716 -
obs--99.97 %
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)
10.40250.23060.00261.51841.33111.3224-0.09490.2037-0.025-0.01990.00350.0891-0.0965-0.13610.09130.712-0.1711-0.08650.3228-0.00850.087376.808-6.224-56.788
20.74070.56750.25860.67090.04250.7446-0.0270.04950.042-0.06760.0473-0.0315-0.3213-0.1708-0.02030.61540.1538-0.00320.13570.02080.255175.60829.312-14.317
30.78850.2911-0.25890.61650.33691.69220.079-0.06640.050.10720.00920.2226-0.1655-0.413-0.08820.46920.17210.04950.23870.02110.273968.5824.9953.463
40.16540.0510.04770.84550.90371.1579-0.14870.1675-0.048-0.18620.15220.059-0.2154-0.0245-0.00340.7233-0.156-0.01930.3388-0.00390.148576.538-1.041-53.594
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A745 - 975
2X-RAY DIFFRACTION2A976 - 1153
3X-RAY DIFFRACTION3A1154 - 1484
4X-RAY DIFFRACTION4A1485 - 1763

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