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- PDB-4jcl: Crystal structure of Alpha-CGT from Paenibacillus macerans at 1.7... -

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Basic information

Entry
Database: PDB / ID: 4jcl
TitleCrystal structure of Alpha-CGT from Paenibacillus macerans at 1.7 Angstrom resolution
ComponentsCyclomaltodextrin glucanotransferase
KeywordsTRANSFERASE / ALPHA BETA BARREL / CALCIUM BINDING / ALPHA CYCLODEXTRIN GLYCOSYLTRANSFERASE
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 / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Cyclomaltodextrin glucanotransferase
Similarity search - Component
Biological speciesPaenibacillus macerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWu, L. / Zhou, J. / Wu, J. / Li, J. / Chen, J.
CitationJournal: To be Published
Title: Crystal Structure of Alpha-Cgt from Paenibacillus Macerans at 1.7 Angstrom Resolution
Authors: Wu, L. / Zhou, J. / Wu, J. / Li, J.
History
DepositionFeb 22, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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_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_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_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: Cyclomaltodextrin glucanotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,18231
Polymers74,0681
Non-polymers2,11430
Water8,359464
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.871, 78.559, 136.820
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, 1 molecules A

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


Mass: 74068.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus macerans (bacteria) / Strain: ATCC 7069 / Gene: cgtM / Plasmid: PET-20B(+) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P04830, cyclomaltodextrin glucanotransferase

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Non-polymers , 7 types, 494 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 464 / 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: 2.39 Å3/Da / Density % sol: 48.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 30% PEG 8000, 0.1M IMIDAZOLE, 0.1M CALCIUM CLORIDE, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 5, 2009
RadiationMonochromator: NUMERICAL LINK TYPE SI(111) DOUBLE CRYSTAL MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 72308 / % possible obs: 91.7 % / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Biso Wilson estimate: 23.89 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 18.25
Reflection shellResolution: 1.7→1.76 Å / % possible all: 91.1

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Processing

Software
NameVersionClassification
CNSrefinement
PHENIX(PHENIX.REFINE: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CGT

1cgt


Resolution: 1.7→47.45 Å / Occupancy max: 1 / Occupancy min: 0.31 / SU ML: 0.49 / σ(F): 1.34 / Phase error: 20.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 3615 5 %
Rwork0.164 --
obs0.166 68613 91.7 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.71 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 129.06 Å2 / Biso mean: 28.82 Å2 / Biso min: 13.89 Å2
Baniso -1Baniso -2Baniso -3
1-2.43 Å2-0 Å20 Å2
2---9.5377 Å20 Å2
3---7.1077 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5228 0 126 464 5818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065508
X-RAY DIFFRACTIONf_angle_d1.0147473
X-RAY DIFFRACTIONf_dihedral_angle_d12.9721911
X-RAY DIFFRACTIONf_chiral_restr0.069809
X-RAY DIFFRACTIONf_plane_restr0.004977
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6999-1.72230.33191070.2976238984
1.7223-1.74590.32611320.2858266193
1.7459-1.77090.30871500.2569276697
1.7709-1.79730.27721400.2411281899
1.7973-1.82540.27041290.21852897100
1.8254-1.85530.2911570.20782792100
1.8553-1.88730.25991720.18832822100
1.8873-1.92160.21631340.17212870100
1.9216-1.95860.21281570.15612826100
1.9586-1.99860.25211440.1628284499
1.9986-2.0420.2111550.1593283499
2.042-2.08950.18841510.153283499
2.0895-2.14180.21431550.15280098
2.1418-2.19970.20271500.1412277897
2.1997-2.26440.21041520.1411277597
2.2644-2.33750.19721690.1471274496
2.3375-2.4210.19341310.1501272895
2.421-2.5180.22641380.1514268593
2.518-2.63250.2251210.1538266891
2.6325-2.77130.17321590.1535245387
2.7713-2.94490.22961310.1485235382
2.9449-3.17230.22161110.1511219875
3.1723-3.49140.21361130.1652203570
3.4914-3.99640.16361000.1621200268
3.9964-5.03420.15761060.1428221474
5.0342-47.46850.19971510.1823282791
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)
10.1496-0.02720.07130.19840.17580.06120.0907-0.09920.10050.06-0.04310.0894-0.060.0378-00.2058-0.0010.02820.2285-0.01460.226-15.976-4.453234.1372
20.06220.0370.0271-0.0027-0.0014-0.0230.01590.0650.2079-0.0247-0.0516-0.0397-0.02330.019600.20280.00470.01180.2214-0.00320.2451-9.41122.113333.0669
30.0075-0.01280.01920.06790.06340.0463-0.05440.009-0.08990.02820.01410.18870.0432-0.1502-0.00010.21760.00250.04080.24380.01390.2745-25.7571-18.549633.511
40.0149-0.0226-0.04420.07650.10420.08810.0408-0.0144-0.0089-0.06940.01130.1595-0.0047-0.0756-00.2190.01070.00120.2521-0.02150.2627-23.5164-6.354427.1053
50.1308-0.02810.0122-0.02470.08890.3165-0.00040.0015-0.0173-0.03280.01650.0324-0.0021-0.0619-00.2038-0.00020.00350.22860.00090.2443-24.4676-14.821620.9088
60.026-0.0325-0.03410.00770.0077-0.0204-0.1313-0.0655-0.184-0.17920.0066-0.11630.12410.2232-00.25850.02170.03150.2290.01370.2589-14.1895-30.582617.5864
70.0829-0.09290.05490.0091-0.02520.00760.04790.03670.0508-0.04010.03360.080.09610.014900.23620.0053-0.00250.2612-0.00320.2101-21.5514-21.137614.6771
80.09140.0125-0.10930.04590.0294-0.024-0.0443-0.0281-0.0038-0.00430.02410.0160.00890.024700.24150.00520.00590.2259-0.00470.2073-15.5659-10.361215.0773
90.0043-0.0064-0.00140.00970.00140.00290.04520.15210.0646-0.0251-0.17070.084-0.15830.1102-0.00010.28760.0131-0.02580.2465-0.00050.2248-12.6285-5.43368.0022
100.0463-0.0142-0.0190.0128-0.00410.015-0.0924-0.0658-0.2265-0.0091-0.1293-0.03080.0461-0.0018-0.00010.24750.00030.0170.24430.00950.2213-7.08-7.864117.6169
110.00320.0076-0.01280.021-0.00250.02980.06490.281-0.07080.09520.005-0.02170.018-0.17010.00020.29270.0138-0.02090.24010.00530.24590.213-23.371324.7736
120.04620.0337-0.04920.02860.00630.06010.00430.0777-0.0213-0.05140.0261-0.01740.0448-0.1663-00.26270.0030.01840.2359-0.01410.2025-0.1584-19.522913.1771
13-0.01260.006-0.15410.28310.28560.21520.02540.0942-0.02260.0008-0.0068-0.1344-0.00540.0700.2097-0.00870.01170.18340.00090.21288.4539-17.037327.3466
140.00350.12490.05580.0159-0.0247-0.01410.07730.00640.0294-0.0626-0.00740.01260.170.2261-00.23710.0110.00410.20560.00610.2055-0.1883-12.616728.0399
150.0573-0.0265-0.0988-0.01410.10260.05360.0546-0.0225-0.049-0.0459-0.0181-0.07250.05770.042600.1928-0.0132-0.00310.2291-0.0030.19773.9064-8.289136.2115
160.01650.04050.06750.00060.0340.06370.0879-0.2814-0.14420.2431-0.0489-0.06290.0293-0.0739-00.2156-0.02280.00270.24920.01370.2377-7.6714-9.321342.3469
170.0120.03470.0199-0.01260.01130.00240.0801-0.15120.2780.0257-0.01930.0426-0.11680.06440.00010.2303-0.00540.02720.2459-0.02670.24964.63222.30535.837
180.23340.1319-0.05190.12290.1580.19540.06380.0407-0.054-0.1471-0.0257-0.12560.10020.075600.1613-00.02340.18510.01740.2217.9089-5.628129.2445
190.060.18590.07770.13850.1690.1166-0.0386-0.2735-0.0899-0.13690.003-0.10720.07930.1967-0.00030.2473-0.00820.05010.2172-0.0180.283722.21082.975933.1722
200.0402-0.05710.02640.1719-0.01410.10640.0564-0.0959-0.0345-0.08750.0381-0.07780.0114-0.1379-0.00010.20640.0060.02760.2057-0.00540.253316.59751.665524.9521
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 4:57)A4 - 57
2X-RAY DIFFRACTION2(chain A and resid 58:78)A58 - 78
3X-RAY DIFFRACTION3(chain A and resid 79:94)A79 - 94
4X-RAY DIFFRACTION4(chain A and resid 95:121)A95 - 121
5X-RAY DIFFRACTION5(chain A and resid 122:177)A122 - 177
6X-RAY DIFFRACTION6(chain A and resid 178:193)A178 - 193
7X-RAY DIFFRACTION7(chain A and resid 194:208)A194 - 208
8X-RAY DIFFRACTION8(chain A and resid 209:240)A209 - 240
9X-RAY DIFFRACTION9(chain A and resid 241:251)A241 - 251
10X-RAY DIFFRACTION10(chain A and resid 252:258)A252 - 258
11X-RAY DIFFRACTION11(chain A and resid 259:265)A259 - 265
12X-RAY DIFFRACTION12(chain A and resid 266:278)A266 - 278
13X-RAY DIFFRACTION13(chain A and resid 279:315)A279 - 315
14X-RAY DIFFRACTION14(chain A and resid 316:334)A316 - 334
15X-RAY DIFFRACTION15(chain A and resid 335:363)A335 - 363
16X-RAY DIFFRACTION16(chain A and resid 364:384)A364 - 384
17X-RAY DIFFRACTION17(chain A and resid 385:399)A385 - 399
18X-RAY DIFFRACTION18(chain A and resid 400:446)A400 - 446
19X-RAY DIFFRACTION19(chain A and resid 447:476)A447 - 476
20X-RAY DIFFRACTION20(chain A and resid 477:508)A477 - 508

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