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- PDB-3zt7: GlgE isoform 1 from Streptomyces coelicolor with beta-cyclodextri... -

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Basic information

Entry
Database: PDB / ID: 3zt7
TitleGlgE isoform 1 from Streptomyces coelicolor with beta-cyclodextrin and maltose bound
ComponentsPUTATIVE GLUCANOHYDROLASE PEP1A
KeywordsHYDROLASE / ALPHA-GLUCAN BIOSYNTHESIS / GLYCOSIDE HYDROLASE FAMILY 13_3
Function / homology
Function and homology information


starch synthase (maltosyl-transferring) / alpha-glucan biosynthetic process / hexosyltransferase activity / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Alpha-amylase domain / Glycosyl hydrolase, family 13, catalytic domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases ...Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Alpha-amylase domain / Glycosyl hydrolase, family 13, catalytic domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Immunoglobulin-like fold / Alpha-Beta Barrel / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / beta-cyclodextrin / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSyson, K. / Stevenson, C.E.M. / Rejzek, M. / Fairhurst, S.A. / Nair, A. / Bruton, C.J. / Field, R.A. / Chater, K.F. / Lawson, D.M. / Bornemann, S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structure of a Streptomyces Maltosyltransferase Glge: A Homologue of a Genetically Validated Anti-Tuberculosis Target.
Authors: Syson, K. / Stevenson, C.E.M. / Rejzek, M. / Fairhurst, S.A. / Nair, A. / Bruton, C.J. / Field, R.A. / Chater, K.F. / Lawson, D.M. / Bornemann, S.
History
DepositionJul 1, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2011Group: Database references
Revision 1.2Nov 9, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AE" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE GLUCANOHYDROLASE PEP1A
B: PUTATIVE GLUCANOHYDROLASE PEP1A
C: PUTATIVE GLUCANOHYDROLASE PEP1A
D: PUTATIVE GLUCANOHYDROLASE PEP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,24112
Polymers310,2594
Non-polymers5,9818
Water6,648369
1
A: PUTATIVE GLUCANOHYDROLASE PEP1A
B: PUTATIVE GLUCANOHYDROLASE PEP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,1206
Polymers155,1302
Non-polymers2,9914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6900 Å2
ΔGint-25.5 kcal/mol
Surface area51660 Å2
MethodPISA
2
C: PUTATIVE GLUCANOHYDROLASE PEP1A
D: PUTATIVE GLUCANOHYDROLASE PEP1A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,1206
Polymers155,1302
Non-polymers2,9914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6840 Å2
ΔGint-25.1 kcal/mol
Surface area51610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.270, 113.380, 315.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A15 - 663
2010B15 - 663
1020A15 - 663
2020C15 - 663
1030A15 - 663
2030D15 - 663
1040B15 - 663
2040C15 - 663
1050B15 - 663
2050D15 - 663
1060C15 - 663
2060D15 - 663

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
PUTATIVE GLUCANOHYDROLASE PEP1A / GLGE ISOFORM 1 / PEP1A / SCO5443 / 1-4-ALPHA-D-


Mass: 77564.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (unknown) / Strain: M145 / Plasmid: PET15B-GLGE1-M145 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: Q9L1K2, Transferases; Glycosyltransferases; Hexosyltransferases, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Polysaccharide
Cycloheptakis-(1-4)-(alpha-D-glucopyranose) / beta-cyclodextrin / Cyclodextrin


Type: oligosaccharide, Oligosaccharide / Class: Drug delivery / Mass: 1153.001 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: cyclic oligosaccharide / References: beta-cyclodextrin
DescriptorTypeProgram
WURCS=2.0/1,7,7/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a1-g4_a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#3: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsINCLUDES AN ADDITIONAL 20 RESIDUES AT THE N-TERMINUS FOR NICKEL AFFINITY PURIFICATION.

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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: 3.26 Å3/Da / Density % sol: 62.8 % / Description: NONE
Crystal growpH: 7 / Details: pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H,K,L10.553
11K,H,-L20.447
ReflectionResolution: 2.5→71.42 Å / Num. obs: 140547 / % possible obs: 99.8 % / Observed criterion σ(I): -9 / Redundancy: 4.9 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.3 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0101refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZST

3zst


Resolution: 2.5→55.8 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.89 / SU B: 9.738 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.068 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.22117 6958 5 %RANDOM
Rwork0.19159 ---
obs0.19305 133513 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1--19.93 Å20 Å20 Å2
2--30.01 Å20 Å2
3----10.09 Å2
Refinement stepCycle: LAST / Resolution: 2.5→55.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20354 0 400 369 21123
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02121393
X-RAY DIFFRACTIONr_bond_other_d0.0060.0214400
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.96729340
X-RAY DIFFRACTIONr_angle_other_deg1.231334866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85352592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11322.525994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.394153062
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.16115204
X-RAY DIFFRACTIONr_chiral_restr0.0930.23310
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02123694
X-RAY DIFFRACTIONr_gen_planes_other0.0050.024466
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A247920.04
12B247920.04
21A249340.03
22C249340.03
31A247320.03
32D247320.03
41B247570.04
42C247570.04
51B246440.03
52D246440.03
61C247180.03
62D247180.03
LS refinement shellResolution: 2.496→2.561 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 485 -
Rwork0.402 9209 -
obs--93.62 %
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)
10.5868-0.17860.4051.077-0.13943.78190.02850.14610.1012-0.0519-0.0349-0.049-0.13170.00950.00640.09040.02040.0120.05550.03760.0643-4.0731-11.44641.6206
23.1419-0.8855-1.80411.9451.48313.03690.00370.23050.0198-0.1602-0.02320.07080.0382-0.17220.01950.15330.0046-0.01120.03230.00710.1373-19.26010.113163.062
32.04530.2332-0.38140.03950.28513.2313-0.23210.09930.1118-0.053-0.01740.0216-0.47250.35010.24950.13630.03270.01140.0860.00960.0830.8195-9.07738.5207
40.9614-0.0268-0.04850.4197-0.04710.5939-0.01590.1301-0.0263-0.06540.01320.00380.01440.03550.00270.09290.00130.00560.24280.02130.07-2.963-24.10886.0742
51.74140.62950.65791.33550.38571.941-0.0351-0.14410.08510.263-0.01420.43880.0137-0.29670.04930.19860.01090.04120.31430.03470.1837-30.3158-27.128224.9457
60.9787-0.19480.38510.6105-0.32873.7582-0.04140.1782-0.0006-0.06060.03990.01070.03240.1470.00140.07160.0167-0.01070.1111-0.01760.100116.4766-32.164136.9472
70.3942-0.3619-0.48083.93740.63413.3065-0.03680.0315-0.01920.15970.018-0.04730.2787-0.10980.01880.2249-0.010.02330.2925-0.04740.224828.114-47.20416.0326
81.6001-0.3559-4.37761.3157-1.221616.91270.22740.17790.09810.0887-0.083-0.1754-0.86590.0126-0.14430.04940.0072-0.0130.1954-0.02280.091219.0817-27.315340.1912
90.3060.02880.08111.1418-0.04880.55040.02850.00560.010.1285-0.00630.02330.01250.038-0.02210.10640.0055-0.00820.003-0.00330.02224.1918-31.039772.7611
101.61591.18350.43472.249-0.00152.3166-0.02920.2161-0.2658-0.40610.06550.01860.44350.0227-0.03620.33450.0421-0.0420.0429-0.04450.15361.1707-58.328753.9442
110.7985-0.20970.26240.87230.33613.5811-0.02150.1605-0.0208-0.0250.0086-0.019-0.14140.04010.0130.07670.0322-0.01470.13320.03460.079650.4754-72.21543.3158
121.85110.1002-0.51921.90331.53382.68-0.09270.0991-0.0399-0.0206-0.13790.14560.0347-0.13930.23060.13010.0176-0.00620.0601-0.01410.098437.5227-62.028866.696
131.17850.1630.54241.14053.261316.01620.27880.11210.1312-0.09590.2842-0.0843-0.14610.7374-0.5630.0985-0.02070.02490.15120.04310.076655.186-69.745140.1106
140.9446-0.07250.04990.31730.0220.974-0.02780.1357-0.0354-0.07940.01430.0015-0.0306-0.02510.01350.0989-0.01630.00320.29130.01150.071149.1385-81.34296.5918
151.25891.0880.78631.63820.04441.6638-0.0213-0.0410.00520.1910.01610.22040.0497-0.14780.00520.2472-0.00290.0620.38150.02690.233422.5895-85.549225.9652
161.1889-0.15740.34330.4942-0.1943.73810.04360.13930.0614-0.0237-0.06620.04750.07610.14210.02260.11020.04350.00580.1706-0.02770.07369.9182-93.235235.6216
170.39150.6182-0.33243.18420.82421.588-0.00930.1022-0.12160.082-0.04840.09060.2057-0.00410.05760.30830.06860.01950.4039-0.04610.237779.7036-106.506212.4985
180.7728-0.19711.69751.6096-5.358119.2858-0.06970.11330.0344-0.01330.04340.007-0.04390.02520.02630.14660.08440.01350.16760.02760.00772.6679-88.739738.9625
190.4187-0.07670.04641.0775-0.16860.65890.00380.0666-0.02630.0822-0.02580.05560.05150.00760.0220.08490.00210.00560.0491-0.01050.021860.1845-94.532272.0776
200.3650.0850.10811.48260.32950.9286-0.04160.1495-0.2503-0.26920.03210.16340.3411-0.10110.00960.3513-0.0356-0.02440.1959-0.0670.258754.3759-120.178151.7525
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 108
2X-RAY DIFFRACTION2A109 - 192
3X-RAY DIFFRACTION3A193 - 205
4X-RAY DIFFRACTION4A206 - 573
5X-RAY DIFFRACTION5A574 - 663
6X-RAY DIFFRACTION6B15 - 108
7X-RAY DIFFRACTION7B109 - 192
8X-RAY DIFFRACTION8B193 - 205
9X-RAY DIFFRACTION9B206 - 573
10X-RAY DIFFRACTION10B574 - 663
11X-RAY DIFFRACTION11C15 - 108
12X-RAY DIFFRACTION12C109 - 192
13X-RAY DIFFRACTION13C193 - 205
14X-RAY DIFFRACTION14C206 - 573
15X-RAY DIFFRACTION15C574 - 663
16X-RAY DIFFRACTION16D15 - 108
17X-RAY DIFFRACTION17D109 - 192
18X-RAY DIFFRACTION18D193 - 205
19X-RAY DIFFRACTION19D206 - 573
20X-RAY DIFFRACTION20D574 - 663

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