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- PDB-5cvs: GlgE isoform 1 from Streptomyces coelicolor E423A mutant soaked i... -

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Basic information

Entry
Database: PDB / ID: 5cvs
TitleGlgE isoform 1 from Streptomyces coelicolor E423A mutant soaked in maltoheptaose
ComponentsAlpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
KeywordsTRANSFERASE / HYDROLASE / 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, 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 / Glycosyl hydrolase, all-beta / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Glycosidases / Glycoside hydrolase superfamily ...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 / 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-maltopentaose / Alpha-1,4-glucan:maltose-1-phosphate maltosyltransferase 1
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRashid, A.M. / Syson, K. / Koliwer-Brandl, H. / van de Weerd, R. / Stevenson, C.E.M. / Batey, S.F.D. / Miah, F. / Alber, M. / Ioerger, T.R. / Chandra, G. ...Rashid, A.M. / Syson, K. / Koliwer-Brandl, H. / van de Weerd, R. / Stevenson, C.E.M. / Batey, S.F.D. / Miah, F. / Alber, M. / Ioerger, T.R. / Chandra, G. / Appelmelk, B.J. / Nartowski, K.P. / Khimyak, Y.Z. / Lawson, D.M. / Jacobs, W.R. / Geurtsen, J. / Kalscheuer, R. / Bornemann, S.
Funding support United Kingdom, Netherlands, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/I012850/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 United Kingdom
Netherlands Organisation for Scientific ResearchV-ICI_81902004 Netherlands
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Ligand-bound structures and site-directed mutagenesis identify the acceptor and secondary binding sites of Streptomyces coelicolor maltosyltransferase GlgE.
Authors: Syson, K. / Stevenson, C.E. / Miah, F. / Barclay, J.E. / Tang, M. / Gorelik, A. / Rashid, A.M. / Lawson, D.M. / Bornemann, S.
History
DepositionJul 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Nov 9, 2016Group: Database references
Revision 1.3Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_struct_assembly_gen / pdbx_validate_close_contact / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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)154,6346
Polymers150,6712
Non-polymers3,9634
Water8,719484
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12670 Å2
ΔGint59 kcal/mol
Surface area50770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.080, 114.080, 314.140
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A15 - 663
2010B15 - 663

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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


Mass: 75335.438 Da / Num. of mol.: 2 / Mutation: E423A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: glgE1, pep1, pep1A, pep1I, SCO5443, SC6A11.19c / Plasmid: PET15B / Details (production host): PET15B-GLGE1-M145 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): PLYSS
References: UniProt: Q9L1K2, starch synthase (maltosyl-transferring)
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a2122h-1a_1-5]/1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltopentaose


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltopentaose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1a_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 484 / 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: 3.39 Å3/Da / Density % sol: 63.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 2.3→62.83 Å / Num. obs: 92902 / % possible obs: 99.9 % / Redundancy: 18.4 % / Biso Wilson estimate: 47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.016 / Net I/σ(I): 27.6 / Num. measured all: 1708887
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.3-2.3617.91.0263.511931166800.8680.24599.4
10.29-62.8316.10.0381.21991012340.9990.00899.5

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Processing

Software
NameVersionClassification
Aimless0.3.6data scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CN6
Resolution: 2.3→62.83 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.2012 / WRfactor Rwork: 0.1725 / FOM work R set: 0.8703 / SU B: 10.055 / SU ML: 0.127 / SU R Cruickshank DPI: 0.211 / SU Rfree: 0.1728 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.211 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2091 4636 5 %RANDOM
Rwork0.1807 ---
obs0.1821 88145 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.36 Å2 / Biso mean: 59.9 Å2 / Biso min: 32.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.52 Å20 Å20 Å2
2--1.52 Å20 Å2
3----3.03 Å2
Refinement stepCycle: final / Resolution: 2.3→62.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10150 0 268 484 10902
Biso mean--80.17 53.31 -
Num. residues----1298
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01910849
X-RAY DIFFRACTIONr_bond_other_d0.0040.029950
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.93514904
X-RAY DIFFRACTIONr_angle_other_deg1.073322867
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.05451322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.67322.361504
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.214151538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.07315106
X-RAY DIFFRACTIONr_chiral_restr0.0780.21698
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02112081
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022543
X-RAY DIFFRACTIONr_mcbond_it0.9932.7025216
X-RAY DIFFRACTIONr_mcbond_other0.9932.7025215
X-RAY DIFFRACTIONr_mcangle_it1.6694.0496523
Refine LS restraints NCS

Ens-ID: 1 / Number: 75692 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 323 -
Rwork0.252 6351 -
all-6674 -
obs--99.27 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.15610.07140.65530.53640.3876.245-0.02930.218-0.0568-0.1006-0.0397-0.09580.25170.45580.0690.29830.11320.09990.1719-0.0110.291142.68-32.151-4.9867
21.6712-0.7455-2.77770.3871.20114.6521-0.2998-0.1202-0.127-0.03140.0418-0.01860.62480.28370.2580.61920.11360.11530.6162-0.14590.524652.4271-42.8865-17.4023
30.9798-0.7901-0.27463.7624-0.28231.6943-0.0226-0.150.05730.3669-0.0278-0.0468-0.0810.0310.05030.3662-0.0319-0.01690.034-0.02940.206534.9111-22.502839.2871
41.14930.0730.2112.2464-0.70721.82660.15750.1272-0.2399-0.2269-0.03510.12240.4883-0.0329-0.12250.4060.0134-0.01950.0184-0.02790.238428.9381-43.269222.7899
51.156-0.0885-0.20951.43640.17796.08050.0010.0706-0.0078-0.0075-0.12540.0857-0.1037-0.13230.12440.24340.04470.00560.0314-0.05190.252921.0762-10.28963.8791
60.4536-0.5886-0.94961.08472.16334.98270.0944-0.04040.0839-0.0707-0.26520.113-0.1152-1.03830.17090.43210.02180.05760.449-0.04550.487611.1868-0.799216.2354
74.7513-1.1315-0.05691.08850.50051.817-0.05910.315-0.1963-0.2787-0.06030.0319-0.030.01430.11930.402-0.01820.0150.3033-0.07270.225925.6124-23.5547-42.2021
81.6038-0.04660.78241.22080.24972.2345-0.0781-0.1779-0.21130.0046-0.04580.2570.0853-0.66690.12390.31760.01080.01020.3552-0.09940.284911.1552-25.4825-22.945
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 115
2X-RAY DIFFRACTION2A116 - 213
3X-RAY DIFFRACTION3A214 - 395
4X-RAY DIFFRACTION4A396 - 663
5X-RAY DIFFRACTION5B15 - 115
6X-RAY DIFFRACTION6B116 - 214
7X-RAY DIFFRACTION7B215 - 361
8X-RAY DIFFRACTION8B362 - 663

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