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- PDB-6l2h: CGTase mutant-Y167H -

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Basic information

Entry
Database: PDB / ID: 6l2h
TitleCGTase mutant-Y167H
ComponentsAlpha-cyclodextrin glucanotransferase
KeywordsSTRUCTURAL PROTEIN / Bacillus sp. 602-1 / Product specificity
Function / homology
Function and homology information


cyclomaltodextrin glucanotransferase / cyclomaltodextrin glucanotransferase activity / starch binding / alpha-amylase activity / transferase 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 / Alpha-cyclodextrin glucanotransferase
Similarity search - Component
Biological speciesPaenibacillus macerans (bacteria)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2.096 Å
AuthorsFan, T.W. / Hou, A.Q. / Chao, Y.P. / Sun, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31171643 China
CitationJournal: To Be Published
Title: Structure basis of a mutant a-CGTase tyrosine167histidine from Bacillus sp. 602-1 with enhanced a-CD production
Authors: Fan, T.W.
History
DepositionOct 3, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Alpha-cyclodextrin glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2123
Polymers74,1311
Non-polymers802
Water9,296516
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.939, 78.448, 135.808
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Alpha-cyclodextrin glucanotransferase / a-CGTase


Mass: 74131.391 Da / Num. of mol.: 1 / Mutation: Y167H,V478T,A536V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus macerans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: S5ZJ19, UniProt: P04830*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 8.5
Details: 15% PEG 4000, 0.05M Tris-HCl, 0.1M sodium acetate buffer, 25mM Na2HPO4, 150mM NaCl, 10mM imidazole, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→39.21 Å / Num. obs: 41763 / % possible obs: 99.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 20.5
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIXv1.0refinement
CrystalCleardata collection
MOSFLMdata reduction
PHASESphasing
RefinementMethod to determine structure: MAD / Resolution: 2.096→39.209 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.57
RfactorNum. reflection% reflection
Rfree0.1948 2106 5.04 %
Rwork0.1565 --
obs0.1584 41763 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 87.55 Å2 / Biso mean: 28.061 Å2 / Biso min: 8.66 Å2
Refinement stepCycle: final / Resolution: 2.096→39.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5233 0 2 516 5751
Biso mean--24.69 35.27 -
Num. residues----687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075359
X-RAY DIFFRACTIONf_angle_d0.9657305
X-RAY DIFFRACTIONf_dihedral_angle_d12.8491847
X-RAY DIFFRACTIONf_chiral_restr0.049799
X-RAY DIFFRACTIONf_plane_restr0.004963
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.096-2.14450.20171210.1612409X-RAY DIFFRACTION92
2.1445-2.19820.23561280.16232668X-RAY DIFFRACTION100
2.1982-2.25760.21691260.16462632X-RAY DIFFRACTION100
2.2576-2.3240.22771570.16612618X-RAY DIFFRACTION100
2.324-2.3990.21521590.16032608X-RAY DIFFRACTION100
2.399-2.48470.18991390.16162612X-RAY DIFFRACTION100
2.4847-2.58420.19711410.16852646X-RAY DIFFRACTION100
2.5842-2.70180.22581430.18042671X-RAY DIFFRACTION100
2.7018-2.84420.24771320.18442643X-RAY DIFFRACTION100
2.8442-3.02230.20341430.18182657X-RAY DIFFRACTION100
3.0223-3.25560.23171440.16992639X-RAY DIFFRACTION100
3.2556-3.5830.18471300.15332678X-RAY DIFFRACTION99
3.583-4.1010.16331510.13112677X-RAY DIFFRACTION99
4.101-5.1650.15391450.12662679X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -4.7484 Å / Origin y: 11.5017 Å / Origin z: -20.0335 Å
111213212223313233
T0.1099 Å2-0.0004 Å20.0016 Å2-0.1035 Å20.0027 Å2--0.1093 Å2
L0.1067 °2-0.0316 °20.0076 °2-0.0695 °20.0665 °2--0.0911 °2
S0.0128 Å °0.0191 Å °-0.0098 Å °-0.001 Å °-0.0182 Å °-0.0114 Å °0.0004 Å °-0.0074 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA32 - 802
2X-RAY DIFFRACTION1allS1 - 516

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