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- PDB-3bmv: Cyclodextrin glycosyl transferase from Thermoanerobacterium therm... -

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Basic information

Entry
Database: PDB / ID: 3bmv
TitleCyclodextrin glycosyl transferase from Thermoanerobacterium thermosulfurigenes EM1 mutant S77P
ComponentsCyclomaltodextrin glucanotransferase
KeywordsTRANSFERASE / glycosidase / thermostable / family 13 glycosyl hydrolas / ligand / substrate / acarbose / Glycosyltransferase / Metal-binding / Secreted
Function / homology
Function and homology information


cyclomaltodextrin glucanotransferase / cyclomaltodextrin glucanotransferase activity / starch binding / alpha-amylase activity / carbohydrate metabolic process / extracellular region / metal ion binding
Similarity search - Function
Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase ...Carbohydrate binding module family 20 / Starch binding domain / CBM20 (carbohydrate binding type-20) domain profile. / Starch binding domain / Carbohydrate-binding-like fold / Alpha-amylase, C-terminal domain / Aamy_C / Alpha-amylase/branching enzyme, C-terminal all beta / Alpha amylase, C-terminal all-beta domain / Alpha amylase / IPT/TIG domain / IPT domain / Alpha amylase, catalytic domain / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycosidases / Immunoglobulin E-set / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cyclomaltodextrin glucanotransferase
Similarity search - Component
Biological speciesThermoanaerobacterium thermosulfurigenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsRozeboom, H.J. / van Oosterwijk, N. / Dijkstra, B.W.
Citation
Journal: Biochem.J. / Year: 2008
Title: Elimination of competing hydrolysis and coupling side reactions of a cyclodextrin glucanotransferase by directed evolution.
Authors: Kelly, R.M. / Leemhuis, H. / Rozeboom, H.J. / van Oosterwijk, N. / Dijkstra, B.W. / Dijkhuizen, L.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: Engineering of cyclodextrin product specificity and pH optima of the thermostable cyclodextrin glycosyltransferase from Thermoanaerobacterium thermosulfurigenes EM1
Authors: Wind, R.D. / Uitdehaag, J.C.M. / Buitelaar, R.M. / Dijkstra, B.W. / Dijkhuizen, L.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structure at 2.3 A resolution and revised nucleotide sequence of the thermostable cyclodextrin glycosyltransferase from Thermonanaerobacterium thermosulfurigenes EM1
Authors: Knegtel, R.M.A. / Wind, R.D. / Rozeboom, H.J. / Kalk, K.H. / Buitelaar, R.M. / Dijkhuizen, L. / Dijkstra, B.W.
History
DepositionDec 13, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclomaltodextrin glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,43712
Polymers75,5081
Non-polymers92911
Water18,4111022
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.625, 96.016, 114.159
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cyclomaltodextrin glucanotransferase / Cyclodextrin-glycosyltransferase / CGTase


Mass: 75508.109 Da / Num. of mol.: 1 / Mutation: S77P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacterium thermosulfurigenes (bacteria)
Strain: EM1 / Gene: amyA / Plasmid: PCSCGT-TT / Production host: Bacillus subtilis (bacteria) / Strain (production host): DB104A
References: UniProt: P26827, cyclomaltodextrin glucanotransferase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1022 / 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: 2.67 Å3/Da / Density % sol: 53.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 20% Ammonium sulfate, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 23, 2007 / Details: Toroidal mirror
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.6→49 Å / Num. all: 95798 / Num. obs: 95798 / % possible obs: 89.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 12.6 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.089 / Net I/σ(I): 14.2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 5.2 / Num. unique all: 8663 / Rsym value: 0.221 / % possible all: 57.2

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Processing

Software
NameVersionClassification
REFMAC5.3.0022refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1A47

1a47


Resolution: 1.6→40.83 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.102 / SU ML: 0.039 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.076 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1633 4793 5 %RANDOM
Rwork0.14225 ---
obs0.14332 95798 89.36 %-
all-95798 --
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: 10.867 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å20 Å2
2--0.09 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5334 0 51 1022 6407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0225574
X-RAY DIFFRACTIONr_angle_refined_deg1.0581.9287626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8925706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38624.639263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.38415824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9741520
X-RAY DIFFRACTIONr_chiral_restr0.0730.2835
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024339
X-RAY DIFFRACTIONr_nbd_refined0.1850.22761
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23927
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2931
X-RAY DIFFRACTIONr_metal_ion_refined0.0640.24
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.250
X-RAY DIFFRACTIONr_mcbond_it0.361.53483
X-RAY DIFFRACTIONr_mcangle_it0.63325563
X-RAY DIFFRACTIONr_scbond_it1.0232414
X-RAY DIFFRACTIONr_scangle_it1.4734.52053
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.179 165 -
Rwork0.154 3883 -
obs--51.86 %
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)
10.41340.08780.17750.69970.06940.18310.02660.0056-0.0794-0.0435-0.0192-0.00340.08430.0282-0.00740.0593-0.0035-0.00730.0220.01440.065850.1992-6.671416.0804
20.8064-0.35630.330.6935-0.0290.4920.07110.0396-0.0929-0.1424-0.04710.07530.0431-0.0344-0.0240.0617-0.01-0.02180.01480.00570.03636.0237-1.84939.8071
30.6458-0.37420.28010.7848-0.12960.56060.0496-0.0187-0.0591-0.0572-0.04080.04170.0223-0.0259-0.00870.0384-0.0084-0.00440.02630.00360.042733.29429.296616.1209
41.65630.0143-0.36380.163-0.23580.62530.04510.02430.15960.0033-0.0258-0.0019-0.04710.013-0.01920.0353-0.0052-0.00230.02580.00320.052352.876620.993313.2877
50.49730.06920.02760.4008-0.00240.5340.0122-0.0104-0.0249-0.0405-0.0015-0.0370.0190.048-0.01070.0367-0.0011-0.00410.03220.01190.052760.34977.318616.5978
60.94270.0039-0.1720.09750.02760.49550.0015-0.12570.05730.01240.0139-0.021-0.03080.0862-0.01530.0314-0.0127-0.01120.0535-0.0020.035863.781718.557530.8012
72.5187-0.34011.05560.85250.12071.9179-0.1232-0.23130.09640.07110.0718-0.0128-0.1467-0.10410.05140.01860.0084-0.01050.0631-0.03440.012542.259321.35439.4249
80.3763-0.18260.1410.7762-0.20350.98190.0117-0.02760.0501-0.0248-0.01810.01550.00970.04050.00640.0218-0.0002-0.00110.0465-0.00050.053924.853728.310614.8668
91.1876-0.6290.01462.2254-0.30951.85670.0068-0.05550.1115-0.02670.0165-0.015-0.12330.0274-0.02330.0141-0.0023-0.00370.0542-0.01870.048219.629131.065316.7811
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 681 - 68
2X-RAY DIFFRACTION2AA69 - 18469 - 184
3X-RAY DIFFRACTION3AA185 - 258185 - 258
4X-RAY DIFFRACTION4AA259 - 315259 - 315
5X-RAY DIFFRACTION5AA316 - 412316 - 412
6X-RAY DIFFRACTION6AA413 - 541413 - 541
7X-RAY DIFFRACTION7AA542 - 579542 - 579
8X-RAY DIFFRACTION8AA580 - 651580 - 651
9X-RAY DIFFRACTION9AA652 - 683652 - 683

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