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- PDB-3aie: Crystal Structure of glucansucrase from Streptococcus mutans -

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Basic information

Entry
Database: PDB / ID: 3aie
TitleCrystal Structure of glucansucrase from Streptococcus mutans
ComponentsGlucosyltransferase-SI
KeywordsTRANSFERASE / beta-alpha-barrels
Function / homology
Function and homology information


dextransucrase activity / dextransucrase / glucan biosynthetic process / glucosyltransferase activity / extracellular region
Similarity search - Function
Glucansucrase / Glucan-binding repeat / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. ...Glucansucrase / Glucan-binding repeat / Glycoside hydrolase, family 70, catalytic domain / Glycosyl hydrolase family 70 / KxYKxGKxW signal peptide / KxYKxGKxW signal peptide / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Glucosyltransferase-SI
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsIto, K. / Ito, S. / Shimamura, T. / Iwata, S.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal structure of glucansucrase from the dental caries pathogen Streptococcus mutans.
Authors: Ito, K. / Ito, S. / Shimamura, T. / Weyand, S. / Kawarasaki, Y. / Misaka, T. / Abe, K. / Kobayashi, T. / Cameron, A.D. / Iwata, S.
History
DepositionMay 12, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 7, 2013Group: Database references
Revision 1.3Mar 13, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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: Glucosyltransferase-SI
B: Glucosyltransferase-SI
C: Glucosyltransferase-SI
D: Glucosyltransferase-SI
E: Glucosyltransferase-SI
F: Glucosyltransferase-SI
G: Glucosyltransferase-SI
H: Glucosyltransferase-SI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)757,52524
Polymers755,6428
Non-polymers1,88316
Water80,1134447
1
A: Glucosyltransferase-SI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6913
Polymers94,4551
Non-polymers2352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glucosyltransferase-SI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6913
Polymers94,4551
Non-polymers2352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Glucosyltransferase-SI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6913
Polymers94,4551
Non-polymers2352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Glucosyltransferase-SI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6913
Polymers94,4551
Non-polymers2352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Glucosyltransferase-SI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6913
Polymers94,4551
Non-polymers2352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Glucosyltransferase-SI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6913
Polymers94,4551
Non-polymers2352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Glucosyltransferase-SI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6913
Polymers94,4551
Non-polymers2352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Glucosyltransferase-SI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6913
Polymers94,4551
Non-polymers2352
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)293.880, 215.416, 218.946
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: 4 / Auth seq-ID: 244 - 1087 / Label seq-ID: 1 - 844

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH

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Components

#1: Protein
Glucosyltransferase-SI


Mass: 94455.297 Da / Num. of mol.: 8 / Fragment: UNP RESIDUES 244-1087
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Gene: gtfC, SMU_1005 / Plasmid: pCold / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P13470, dextransucrase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 4447 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsUNP SHOWS VARIANT AT THESE POSITIONS

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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: 4.59 Å3/Da / Density % sol: 73.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M ammonium sulfate, 0.1M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 98 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 753230 / % possible obs: 99.58 % / Redundancy: 7 %
Reflection shellResolution: 2.102→2.157 Å / Rmerge(I) obs: 0.212 / Num. unique all: 54729 / % possible all: 98.43

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
REFMAC5.5.0066refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.654 / SU ML: 0.093 / Cross valid method: THROUGHOUT / σ(I): 2 / ESU R Free: 0.141 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23566 39655 5 %RANDOM
Rwork0.20283 ---
obs0.20448 753230 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.507 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms53279 0 104 4447 57830
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.02254511
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2751.94374038
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.00856744
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94225.0452664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.047159096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7815256
X-RAY DIFFRACTIONr_chiral_restr0.1990.28144
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.02141876
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_it1.11.525205
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.669240618
X-RAY DIFFRACTIONr_scbond_it3.015315669
X-RAY DIFFRACTIONr_scangle_it4.3144.514897
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 6659 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.250.5
Bmedium positional0.340.5
Cmedium positional0.230.5
Dmedium positional0.240.5
Emedium positional0.350.5
Fmedium positional0.30.5
Gmedium positional0.270.5
Hmedium positional0.240.5
Amedium thermal1.322
Bmedium thermal1.412
Cmedium thermal1.272
Dmedium thermal1.432
Emedium thermal1.382
Fmedium thermal1.42
Gmedium thermal22
Hmedium thermal1.92
LS refinement shellResolution: 2.102→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 2833 -
Rwork0.212 54729 -
obs--98.43 %
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)
10.3506-0.1259-0.19320.76680.16370.61330.0449-0.0650.0842-0.0044-0.0199-0.0655-0.09510.1263-0.02510.0309-0.0321-0.01640.05790.00560.0593194.06651.664192.998
20.43110.042-0.0470.5228-0.23240.60160.0098-0.0346-0.00850.05340.05560.02-0.1218-0.0946-0.06540.1140.12580.06760.14740.07480.1428246.265-5.141191.988
30.30790.2126-0.14430.8093-0.25660.40470.01050.00340.06050.10150.01410.0475-0.1263-0.0689-0.02460.094-0.02140.00070.078-0.00260.0358246.82256.538135.24
40.4117-0.0850.00050.52310.29780.5205-0.04610.0673-0.0378-0.15430.0289-0.0345-0.10760.05210.01720.0917-0.04580.04460.06410.00770.074194.535-0.459136.394
50.42860.06890.26950.44580.19660.78850.0084-0.10840.03880.1886-0.01670.03540.0407-0.03280.00830.0974-0.01340.00710.05380.00830.0397173.00825.482218.68
60.3949-0.09790.04750.6097-0.27050.57750.01460.0517-0.0976-0.15280.00080.04770.1144-0.0321-0.01540.15070.05050.08110.14090.02040.1479267.465-30.865166.965
70.39220.07350.10510.51370.28950.6345-0.00120.0228-0.07660.0131-0.0358-0.02440.06040.00140.03710.01750.00050.03130.02960.01080.0833173.748-26.499161.715
80.3064-0.0920.24180.4592-0.27910.92440.01780.060.0166-0.0739-0.0284-0.06490.11670.07550.01060.0626-0.01950.01480.0604-0.00580.0546267.28530.201109.447
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A244 - 1087
2X-RAY DIFFRACTION2B244 - 1087
3X-RAY DIFFRACTION3C244 - 1087
4X-RAY DIFFRACTION4D244 - 1087
5X-RAY DIFFRACTION5E244 - 1087
6X-RAY DIFFRACTION6F244 - 1087
7X-RAY DIFFRACTION7G244 - 1087
8X-RAY DIFFRACTION8H244 - 1087

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