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- PDB-4cn4: GlgE isoform 1 from Streptomyces coelicolor E423A mutant with 2-d... -

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Basic information

Entry
Database: PDB / ID: 4cn4
TitleGlgE isoform 1 from Streptomyces coelicolor E423A mutant with 2-deoxy- 2-fluoro-beta-maltosyl modification
ComponentsALPHA-1,4-GLUCAN\:MALTOSE-1-PHOSPHATE MALTOSYLTRANSFERASE 1
KeywordsTRANSFERASE / ALPHA-GLUCAN BIOSYNTHESIS / GLYCOSIDE HYDROLASE FAMILY 13_3 / DRUG TARGET
Function / homology
Function and homology information


starch synthase (maltosyl-transferring) / alpha-glucan biosynthetic process / oligosaccharide catabolic process / hexosyltransferase activity / alpha-amylase activity
Similarity search - Function
: / GLGE, C-terminal / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta ...: / GLGE, C-terminal / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase, domain N/S / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Glycosyl hydrolase, family 13, catalytic domain / Alpha-amylase domain / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSyson, K. / Stevenson, C.E.M. / Rashid, A.M. / Saalbach, G. / Tang, M. / Tuukanen, A. / Svergun, D.I. / Withers, S.G. / Lawson, D.M. / Bornemann, S.
CitationJournal: Biochemistry / Year: 2014
Title: Structural Insight Into How Streptomyces Coelicolor Maltosyl Transferase Glge Binds Alpha-Maltose 1-Phosphate and Forms a Maltosyl-Enzyme Intermediate.
Authors: Syson, K. / Stevenson, C.E.M. / Rashid, A.M. / Saalbach, G. / Tang, M. / Tuukkanen, A. / Svergun, D.I. / Withers, S.G. / Lawson, D.M. / Bornemann, S.
History
DepositionJan 21, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ALPHA-1,4-GLUCAN\:MALTOSE-1-PHOSPHATE MALTOSYLTRANSFERASE 1
B: ALPHA-1,4-GLUCAN\:MALTOSE-1-PHOSPHATE MALTOSYLTRANSFERASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,7024
Polymers155,0142
Non-polymers6892
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-16.4 kcal/mol
Surface area50520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.000, 113.000, 312.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein ALPHA-1,4-GLUCAN\:MALTOSE-1-PHOSPHATE MALTOSYLTRANSFERASE 1 / GMPMT 1 / (1->4)-ALPHA-D-GLUCAN MALTOSE-1-PHOSPHATE ALPHA-D-MALTOSYLTRANSFERASE 1 / PEP1A / SCO5443 ...GMPMT 1 / (1->4)-ALPHA-D-GLUCAN MALTOSE-1-PHOSPHATE ALPHA-D-MALTOSYLTRANSFERASE 1 / PEP1A / SCO5443 / 1-4-ALPHA-D- GLUCAN PHOSPHATE ALPHA-D-MALTOSYLTRANSFERASE / GLGE ISOFORM 1


Mass: 77506.812 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Strain: M145 / Plasmid: PET15B-GLGE1-M145 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: Q9L1K2, starch synthase (maltosyl-transferring)
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-2-deoxy-2-fluoro-beta-D-glucopyranose


Type: oligosaccharide / Mass: 344.288 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*F][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Glcp2fluoro]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsINCLUDES AN ADDITIONAL 20 RESIDUES AT THE N-TERMINUS FOR NICKEL AFFINITY PURIFICATION. RESIDUE 423 ...INCLUDES AN ADDITIONAL 20 RESIDUES AT THE N-TERMINUS FOR NICKEL AFFINITY PURIFICATION. RESIDUE 423 MUTATED FROM GLU TO ALA.

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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: 62.3 % / 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: I04-1 / Wavelength: 0.917
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.4→50.54 Å / Num. obs: 79517 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 43.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.7
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.99 / Mean I/σ(I) obs: 2 / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZSS

3zss


Resolution: 2.4→50.54 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 12.12 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20848 3985 5 %RANDOM
Rwork0.184 ---
obs0.18525 75425 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2--0.88 Å20 Å2
3----1.77 Å2
Refinement stepCycle: LAST / Resolution: 2.4→50.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10162 0 44 418 10624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910577
X-RAY DIFFRACTIONr_bond_other_d0.0040.029755
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.94914494
X-RAY DIFFRACTIONr_angle_other_deg0.9073.00222392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.86551310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.85622.349498
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38151542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.48115106
X-RAY DIFFRACTIONr_chiral_restr0.0770.21592
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112031
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022521
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_it1.0882.1475204
X-RAY DIFFRACTIONr_mcbond_other1.0882.1475203
X-RAY DIFFRACTIONr_mcangle_it1.7473.2196505
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3342.285373
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
LS refinement shellResolution: 2.403→2.466 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 286 -
Rwork0.335 5232 -
obs--95.25 %
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)
11.26050.05390.7790.76040.22586.8326-0.01750.2475-0.0366-0.0788-0.1-0.10850.27060.50320.11750.24520.0940.05630.2383-0.01890.232142.2446-32.3023-4.8789
25.42670.8822-0.6464.4405-0.66345.9101-0.2732-0.178-0.41310.229-0.13920.09320.49260.15380.41240.61630.12520.13590.5469-0.0580.484753.5814-47.2079-25.436
30.5064-0.05620.15141.1456-0.03411.29760.0439-0.00440.02120.2788-0.0216-0.00710.00650.0291-0.02230.37310.0054-0.00570.0069-0.0010.168832.2796-29.035231.7447
42.9351.42320.68112.8007-0.4980.73520.14610.3072-0.5684-0.4454-0.0031-0.07440.61150.1051-0.1430.76380.0485-0.04840.1007-0.06960.272429.6138-55.427415.5484
50.4778-0.0935-0.00941.8560.72445.97830.0080.09140.0044-0.0618-0.11810.0573-0.2034-0.11450.11010.23810.05180.01150.0701-0.03210.203120.9359-10.69253.987
67.20290.3501-1.49634.51540.21877.91160.00980.44050.19140.0030.07570.24110.152-1.0614-0.08550.36970.03190.07610.394-0.01910.41517.06371.582825.1891
70.53060.06830.04140.63960.66442.6798-0.08640.3076-0.0645-0.25010.0067-0.0071-0.27990.08960.07970.3196-0.01270.0070.2912-0.02790.221126.7962-19.9172-34.4635
81.49160.13130.94831.24510.33062.621-0.0179-0.2675-0.19780.1199-0.11660.38770.1845-0.9540.13450.2707-0.03390.02060.5488-0.08940.30975.1066-27.6912-21.5548
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 115
2X-RAY DIFFRACTION2A116 - 189
3X-RAY DIFFRACTION3A190 - 557
4X-RAY DIFFRACTION4A558 - 663
5X-RAY DIFFRACTION5B15 - 115
6X-RAY DIFFRACTION6B116 - 189
7X-RAY DIFFRACTION7B190 - 425
8X-RAY DIFFRACTION8B426 - 663

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