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- PDB-6aij: Cyclodextrin glycosyltransferase from Paenibacillus macerans muta... -

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Basic information

Entry
Database: PDB / ID: 6aij
TitleCyclodextrin glycosyltransferase from Paenibacillus macerans mutant N603D
ComponentsCyclomaltodextrin glucanotransferase
KeywordsSUGAR BINDING PROTEIN / Cyclodextrin glycosyltransferase / Paenibacillus macerans
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 / IPT/TIG domain / IPT domain ...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 / 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 / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cyclomaltodextrin glucanotransferase
Similarity search - Component
Biological speciesPaenibacillus macerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.096 Å
AuthorsLi, C.M. / Ban, X.F. / Li, Z.F. / Li, Y.L. / Cheng, S.D. / Zhang, C.Y. / Jin, T.C. / Gu, Z.B.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31722040 China
National Natural Science Foundation of China31771935 China
CitationJournal: To Be Published
Title: Cyclodextrin glycosyltransferase from Paenibacillus macerans mutant N603D
Authors: Ban, X.F. / Gu, Z.B. / Li, Z.F. / Li, Y.L. / Li, C.M. / Cheng, S.D. / Zhang, C.Y. / Jin, T.C.
History
DepositionAug 24, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclomaltodextrin glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2565
Polymers76,0961
Non-polymers1604
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area330 Å2
ΔGint-40 kcal/mol
Surface area23530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.350, 102.350, 115.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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


Mass: 76095.789 Da / Num. of mol.: 1 / Mutation: N604D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus macerans (bacteria) / Gene: cgtM / Production host: Escherichia coli (E. coli)
References: UniProt: P04830, cyclomaltodextrin glucanotransferase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSequence conflicts G156A/M157L (residue numbering in coordinates) were observed in AAA22298 (PubMed: ...Sequence conflicts G156A/M157L (residue numbering in coordinates) were observed in AAA22298 (PubMed:3011735) according to sequence reference UniProtKB P04830 (CDGT1_PAEMA).

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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: 2.29 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% PEG 4000, 0.1M Tris-HCl pH 9.0, 0.1M Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 2.096→48.386 Å / Num. obs: 39832 / % possible obs: 98.88 % / Redundancy: 6 % / Biso Wilson estimate: 35.88 Å2 / Net I/σ(I): 2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2.096→48.386 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.58
RfactorNum. reflection% reflection
Rfree0.2373 1996 5.01 %
Rwork0.1807 --
obs0.1836 39832 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.096→48.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5229 0 4 22 5255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075381
X-RAY DIFFRACTIONf_angle_d0.8467342
X-RAY DIFFRACTIONf_dihedral_angle_d2.6754180
X-RAY DIFFRACTIONf_chiral_restr0.053804
X-RAY DIFFRACTIONf_plane_restr0.005969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0956-2.1480.38641230.322365X-RAY DIFFRACTION87
2.148-2.20610.30871420.2332728X-RAY DIFFRACTION100
2.2061-2.2710.35851390.27322688X-RAY DIFFRACTION98
2.271-2.34430.2851400.22642699X-RAY DIFFRACTION99
2.3443-2.42810.28581470.20822713X-RAY DIFFRACTION100
2.4281-2.52530.3021460.21272732X-RAY DIFFRACTION100
2.5253-2.64020.27731390.21072727X-RAY DIFFRACTION100
2.6402-2.77940.2981450.21992741X-RAY DIFFRACTION100
2.7794-2.95360.29651410.21532705X-RAY DIFFRACTION100
2.9536-3.18160.30731460.22592741X-RAY DIFFRACTION100
3.1816-3.50160.25181420.19682733X-RAY DIFFRACTION100
3.5016-4.00810.21561510.16192733X-RAY DIFFRACTION100
4.0081-5.0490.15211450.12492750X-RAY DIFFRACTION100
5.049-48.39920.17091500.13092781X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 24.2854 Å / Origin y: -43.8747 Å / Origin z: -4.8623 Å
111213212223313233
T0.1868 Å2-0.0088 Å2-0.0096 Å2-0.2203 Å20.0061 Å2--0.1938 Å2
L0.8978 °2-0.5966 °2-0.0628 °2-1.1022 °2-0.0673 °2--0.379 °2
S0.0263 Å °0.0724 Å °-0.0975 Å °-0.0452 Å °-0.0408 Å °0.2014 Å °0.0355 Å °0.0202 Å °-0.0005 Å °
Refinement TLS groupSelection details: all

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