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- PDB-3sey: Zn-mediated Polymer of Maltose-binding Protein A216H/K220H by Syn... -

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Basic information

Entry
Database: PDB / ID: 3sey
TitleZn-mediated Polymer of Maltose-binding Protein A216H/K220H by Synthetic Symmetrization (Form II)
ComponentsMaltose-binding periplasmic protein
KeywordsSUGAR BINDING PROTEIN / metal-mediated synthetic symmetrization / synthetic symmetrization
Function / homology
Function and homology information


detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis ...detection of maltose stimulus / maltose binding / maltose transport complex / maltose transport / maltodextrin transmembrane transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / carbohydrate transport / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response / membrane
Similarity search - Function
Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-maltose / ACETATE ION / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsZhao, M. / Soriaga, A.B. / Laganowsky, A. / Sawaya, M.R. / Cascio, D. / Yeates, T.O.
CitationJournal: Protein Sci. / Year: 2011
Title: An approach to crystallizing proteins by metal-mediated synthetic symmetrization.
Authors: Laganowsky, A. / Zhao, M. / Soriaga, A.B. / Sawaya, M.R. / Cascio, D. / Yeates, T.O.
History
DepositionJun 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2011Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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: Maltose-binding periplasmic protein
C: Maltose-binding periplasmic protein
E: Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,55842
Polymers122,0943
Non-polymers3,46439
Water8,647480
1
A: Maltose-binding periplasmic protein
hetero molecules

A: Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,29636
Polymers81,3962
Non-polymers2,90034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5480 Å2
ΔGint-385 kcal/mol
Surface area30040 Å2
MethodPISA
2
C: Maltose-binding periplasmic protein
E: Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,41024
Polymers81,3962
Non-polymers2,01422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-289 kcal/mol
Surface area29570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.660, 63.650, 221.830
Angle α, β, γ (deg.)90.000, 90.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 6 molecules ACE

#1: Protein Maltose-binding periplasmic protein / MMBP / Maltodextrin-binding protein


Mass: 40698.020 Da / Num. of mol.: 3 / Mutation: A216H, K220H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b4034, JW3994, malE / Plasmid: pMal-a1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P0AEX9
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
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

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Non-polymers , 4 types, 516 molecules

#3: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 480 / 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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M MES, 0.2M ZINC ACETATE, 10% (W/V) PEG 8000, pH 8.0, vapor diffusion, hanging drop, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 16, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.85→99.76 Å / Num. obs: 119829 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.717 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.04
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.85-1.90.5372.32533141644494.7
1.9-1.950.4363.21704831686399.5
1.95-2.010.3274.24697341648699.6
2.01-2.070.2575.35687401591799.5
2.07-2.140.2116.4680951555399.5
2.14-2.210.1777.57663821490099.6
2.21-2.290.1558.62657701450699.7
2.29-2.390.1349.96639171383899.7
2.39-2.490.12211.07627851334699.8
2.49-2.620.11112.24607941270199.8
2.62-2.760.09814.01587461208399.8
2.76-2.930.0915.5571101151599.9
2.93-3.130.08416.87546431083999.8
3.13-3.380.07818.8451145997499.8
3.38-3.70.07220.33483199313100
3.7-4.140.06621.25436848263100
4.14-4.780.0622.3739855736999.9
4.78-5.850.0622.2734035623099.9
5.85-8.270.05622.4526050480899.9
8.270.04722.213267260398.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.9 Å73.94 Å
Translation1.9 Å73.94 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→49.094 Å / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.8243 / SU ML: 0.55 / σ(F): 2 / Phase error: 25.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 5992 5 %
Rwork0.2085 --
obs0.2104 119829 99.76 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.81 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 120.97 Å2 / Biso mean: 31.4836 Å2 / Biso min: 4.61 Å2
Baniso -1Baniso -2Baniso -3
1--0.6494 Å2-0 Å20.6138 Å2
2---0.907 Å20 Å2
3---1.5565 Å2
Refinement stepCycle: LAST / Resolution: 1.85→49.094 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8538 0 154 480 9172
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078974
X-RAY DIFFRACTIONf_angle_d1.04812216
X-RAY DIFFRACTIONf_chiral_restr0.0741347
X-RAY DIFFRACTIONf_plane_restr0.0051581
X-RAY DIFFRACTIONf_dihedral_angle_d12.6843254
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.87090.34351910.28613626381795
1.8709-1.8930.32471920.28183658385098
1.893-1.9160.32272020.264338264028100
1.916-1.94030.29951980.266437573955100
1.9403-1.96580.30531990.254437963995100
1.9658-1.99280.29142000.246837953995100
1.9928-2.02120.26981950.237237093904100
2.0212-2.05140.28732060.236939024108100
2.0514-2.08350.28541930.230736663859100
2.0835-2.11760.28822030.235838624065100
2.1176-2.15410.28921970.229937433940100
2.1541-2.19330.27312010.228338214022100
2.1933-2.23550.27611970.222337373934100
2.2355-2.28110.2812010.227838294030100
2.2811-2.33070.27491960.227837303926100
2.3307-2.38490.27522040.217338614065100
2.3849-2.44460.28261970.226737563953100
2.4446-2.51070.24682000.218837863986100
2.5107-2.58450.30552010.228438214022100
2.5845-2.6680.26482000.212737973997100
2.668-2.76330.23571990.208837913990100
2.7633-2.87390.27512000.212437963996100
2.8739-3.00470.25612020.224538464048100
3.0047-3.16310.26622010.218938104011100
3.1631-3.36120.22112010.212838144015100
3.3612-3.62070.24711990.200437853984100
3.6207-3.98490.21362040.183938834087100
3.9849-4.56120.17472020.154938364038100
4.5612-5.74520.18482020.155338474049100
5.7452-49.11090.21952090.19723951416099
Refinement TLS params.Method: refined / Origin x: 29.3341 Å / Origin y: 0.9869 Å / Origin z: 55.6098 Å
111213212223313233
T-0.2514 Å20.3009 Å20.1052 Å2--0.2202 Å2-0.087 Å2---0.1772 Å2
L0.2576 °2-0.0271 °2-0.0188 °2-0.2402 °20.126 °2--0.066 °2
S0.105 Å °-0.083 Å °0.0865 Å °0.4845 Å °-0.0788 Å °0.3046 Å °-0.02 Å °0.0178 Å °0.0037 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 371
3X-RAY DIFFRACTION1ALLC1 - 371
5X-RAY DIFFRACTION1ALLE1 - 370

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