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- PDB-4ayg: Lactobacillus reuteri N-terminally truncated glucansucrase GTF180... -

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Basic information

Entry
Database: PDB / ID: 4ayg
TitleLactobacillus reuteri N-terminally truncated glucansucrase GTF180 in orthorhombic apo-form
ComponentsGLUCANSUCRASE
KeywordsTRANSFERASE / GLYCOSYLTRANSFERASE / GLYCOSYL HYDROLASE FAMILY 70 / CIRCULARLY PERMUTED BETA-ALPHA BARREL
Function / homology
Function and homology information


dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / metal ion binding
Similarity search - Function
Glucansucrase / Cholin Binding / left handed beta-beta-3-solenoid / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Choline-binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. ...Glucansucrase / Cholin Binding / left handed beta-beta-3-solenoid / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Choline-binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Ribbon / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / ISOPROPYL ALCOHOL / dextransucrase
Similarity search - Component
Biological speciesLACTOBACILLUS REUTERI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPijning, T. / Vujicic-Zagar, A. / Kralj, S. / Dijkhuizen, L. / Dijkstra, B.W.
CitationJournal: FEBS J. / Year: 2014
Title: Flexibility of Truncated and Full-Length Glucansucrase Gtf180 Enzymes from Lactobacillus Reuteri 180.
Authors: Pijning, T. / Vujicic-Zagar, A. / Kralj, S. / Dijkhuizen, L. / Dijkstra, B.W.
History
DepositionJun 21, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2May 14, 2014Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 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_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_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_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
B: GLUCANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,53595
Polymers233,4712
Non-polymers8,06493
Water39,4172188
1
A: GLUCANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,41255
Polymers116,7361
Non-polymers4,67654
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GLUCANSUCRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,12340
Polymers116,7361
Non-polymers3,38739
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.792, 147.363, 244.374
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein GLUCANSUCRASE /


Mass: 116735.633 Da / Num. of mol.: 2 / Fragment: N-TERMINALLY TRUNCATED GTF180, RESIDUES 742-1772
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOBACILLUS REUTERI (bacteria) / Strain: 180 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: Q5SBN3, dextransucrase

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Non-polymers , 6 types, 2281 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 55 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H4O2
#6: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2188 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONFLICT F1674L MAY BE DUE TO PCR ERROR

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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: 3.58 Å3/Da / Density % sol: 65.6 % / Description: NONE
Crystal growpH: 6.5
Details: 2.2 M (NH4)2SO4, 5% (V/V) 2-PROPANOL, 25 MM HAC/NAAC PH 5.0, 50 MM NACL, 1 MM CACL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.1053
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1053 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 201509 / % possible obs: 93.8 % / Observed criterion σ(I): 3.1 / Redundancy: 6.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.7
Reflection shellResolution: 2→2.09 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.1 / % possible all: 69.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
HKLdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3KLK

3klk


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.752 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.117 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.18306 10644 5 %RANDOM
Rwork0.15482 ---
obs0.15625 201509 93.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 18.891 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.19 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16272 0 497 2188 18957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0217126
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.271.95323206
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.00852076
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23725.499891
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.295152685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3861570
X-RAY DIFFRACTIONr_chiral_restr0.0870.22508
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113222
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: 1.999→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 515 -
Rwork0.206 10129 -
obs--65.98 %
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)
10.7251-0.1263-0.12740.9561-0.15140.50850.0301-0.00380.01010.0126-0.02060.1039-0.0736-0.0208-0.00950.03010.0159-0.00020.0110.00010.047422.93220.812-11.6
20.1835-0.12980.00780.3198-0.07360.17090.01050.0203-0.02090.0002-0.01830.02790.0028-0.0040.00780.0026-0.00280.00040.0109-0.00230.034139.341-11.842-8.177
31.27820.6073-0.29720.6404-0.26360.57820.0331-0.0844-0.12690.0156-0.0412-0.06560.0038-0.00090.0080.0026-0.0011-0.00460.01720.02820.057739.221-53.38915.627
40.5134-0.40530.02820.9022-0.27651.3295-0.0282-0.13580.04360.15520.0618-0.0271-0.1410.0115-0.03360.0426-0.0150.00650.0681-0.0210.021544.082-28.46732.616
51.32630.02460.45320.60040.14360.98050.00770.05930.0732-0.0688-0.01490.102-0.017-0.03770.00720.0353-0.0079-0.02170.01080.00610.043550.18626.8275.106
60.3792-0.10340.28270.1716-0.02850.68340.0212-0.0416-0.06180.01890.02030.00490.09530.0815-0.04150.04440.00590.0010.03820.0120.024275.30818.23430.519
70.92930.0988-0.11410.3806-0.14831.26840.03510.1019-0.0325-0.0255-0.01540.00420.09960.0069-0.01970.06220.0378-0.01390.062-0.01210.00482.51812.75977.414
80.6793-0.17770.01490.68960.10251.18790.0102-0.00360.08450.024-0.0544-0.0551-0.1375-0.13170.04420.08370.02370.01380.06140.02290.031775.15240.67868.72
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1239 - 1375
2X-RAY DIFFRACTION2A926 - 1240
3X-RAY DIFFRACTION2A1376 - 1602
4X-RAY DIFFRACTION3A793 - 927
5X-RAY DIFFRACTION3A1603 - 1636
6X-RAY DIFFRACTION4A742 - 788
7X-RAY DIFFRACTION4A1635 - 1770
8X-RAY DIFFRACTION5B1239 - 1375
9X-RAY DIFFRACTION6B926 - 1240
10X-RAY DIFFRACTION6B1376 - 1602
11X-RAY DIFFRACTION7B792 - 927
12X-RAY DIFFRACTION7B1603 - 1636
13X-RAY DIFFRACTION8B742 - 791
14X-RAY DIFFRACTION8B1635 - 1771

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