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- PDB-4cn1: GlgE isoform 1 from Streptomyces coelicolor D394A mutant with mal... -

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Basic information

Entry
Database: PDB / ID: 4cn1
TitleGlgE isoform 1 from Streptomyces coelicolor D394A mutant with maltose- 1-phosphate bound
ComponentsALPHA-1,4-GLUCAN\: MALTOSE-1-PHOSPHATE MALTOSYLTRANSFERASE 1
KeywordsHYDROLASE / 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-maltose 1-phosphate / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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 / 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 / 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.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_database_status.status_code_sf
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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BE" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BE" 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: 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)155,8864
Polymers155,0422
Non-polymers8452
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4400 Å2
ΔGint-15.6 kcal/mol
Surface area51220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.520, 113.520, 313.600
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 / GLGE ISOFORM 1 / PEP1A / SCO5443 / (1->4)-ALPHA-D-GLUCAN\:MALTOSE-1-PHOSPHATE ALPHA-D- ...GMPMT 1 / GLGE ISOFORM 1 / PEP1A / SCO5443 / (1->4)-ALPHA-D-GLUCAN\:MALTOSE-1-PHOSPHATE ALPHA-D-MALTOSYLTRANSFERASE / 1-4-ALPHA-D-GLUCAN\:PHOSPHATE ALPHA-D-MALTOSYLTRANSFERASE


Mass: 77520.836 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)-1-O-phosphono-alpha-D-glucopyranose / alpha-maltose 1-phosphate


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 422.277 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose 1-phosphate
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a2122h-1a_1-5_1*OPO/3O/3=O][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][P]{[(0+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 437 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsINCLUDES AN ADDITIONAL 20 RESIDUES AT THE N-TERMINUS FOR NICKEL AFFINITY PURIFICATION. RESIDUE 394 ...INCLUDES AN ADDITIONAL 20 RESIDUES AT THE N-TERMINUS FOR NICKEL AFFINITY PURIFICATION. RESIDUE 394 MUTATED FROM ASP 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: I24 / Wavelength: 0.978
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.55→104.53 Å / Num. obs: 67726 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 14 % / Biso Wilson estimate: 54.1 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 11.4
Reflection shellResolution: 2.55→2.62 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3 / % possible all: 96.6

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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: 2.55→91.95 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.923 / SU B: 14.495 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.343 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21507 3423 5.1 %RANDOM
Rwork0.18462 ---
obs0.18616 64195 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20 Å2
2--0.24 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.55→91.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10221 0 54 437 10712
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910667
X-RAY DIFFRACTIONr_bond_other_d0.0040.029867
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.94914615
X-RAY DIFFRACTIONr_angle_other_deg0.909322652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04851315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56222.198514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.528151572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.77215115
X-RAY DIFFRACTIONr_chiral_restr0.0760.21597
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02112121
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022568
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_it1.1682.3465210
X-RAY DIFFRACTIONr_mcbond_other1.1682.3465209
X-RAY DIFFRACTIONr_mcangle_it1.8933.5166514
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5032.5315457
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: 2.55→2.616 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 227 -
Rwork0.275 4520 -
obs--96.6 %
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)
11.63760.21780.91120.67010.66476.77330.03240.1922-0.0134-0.0567-0.0306-0.09490.03980.3651-0.00180.08770.06940.04060.08880.00770.136542.1382-32.1274-4.223
24.76971.02560.07864.61910.80396.6831-0.0274-0.1275-0.34670.2602-0.0557-0.04390.2860.25920.08310.29580.06480.06820.2994-0.00070.368553.4113-47.4075-25.6108
30.4998-0.226-0.08690.87760.18391.2706-0.019-0.06390.03490.27240.0136-0.0336-0.04660.01150.00540.1817-0.0178-0.01680.0114-0.00790.107135.5809-23.955234.892
40.88490.1350.0691.7893-0.62111.60510.08620.1335-0.1781-0.19290.0050.08510.3962-0.0926-0.09120.1954-0.0061-0.03840.0297-0.01820.106928.5514-44.988922.7739
51.0876-0.04620.09411.14270.52486.4851-0.04420.08680.0006-0.003-0.07220.0178-0.2681-0.07430.11650.13760.057-0.02160.0439-0.03420.113421.2435-11.00643.1923
68.2753-0.5023-1.38673.7653-0.61558.99040.05640.56830.1393-0.10730.14710.19490.1372-0.6521-0.20350.19510.02330.01180.2474-0.03350.26617.11271.402924.9611
70.5312-0.1019-0.05410.47610.57812.1669-0.04910.2137-0.035-0.1341-0.0362-0.0293-0.17560.0420.08540.1586-0.00940.00920.1486-0.00560.15626.5291-19.9584-34.6395
81.7820.19760.87370.98950.06121.9162-0.003-0.3472-0.18310.1778-0.02460.30810.153-0.74240.02760.1268-0.01490.01720.387-0.02440.214.8303-28.024-21.5015
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 113
2X-RAY DIFFRACTION2A114 - 190
3X-RAY DIFFRACTION3A191 - 404
4X-RAY DIFFRACTION4A405 - 663
5X-RAY DIFFRACTION5B15 - 113
6X-RAY DIFFRACTION6B114 - 189
7X-RAY DIFFRACTION7B190 - 424
8X-RAY DIFFRACTION8B425 - 663

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