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- PDB-3set: Ni-mediated Dimer of Maltose-binding Protein A216H/K220H by Synth... -

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Basic information

Entry
Database: PDB / ID: 3set
TitleNi-mediated Dimer of Maltose-binding Protein A216H/K220H by Synthetic Symmetrization (Form I)
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 / carbohydrate transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / 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 / carbohydrate transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / outer membrane-bounded periplasmic space / periplasmic space / DNA damage response
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 / NICKEL (II) ION / Maltose/maltodextrin-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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.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.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_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_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_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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,1986
Polymers81,3962
Non-polymers8024
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0993
Polymers40,6981
Non-polymers4012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Maltose-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0993
Polymers40,6981
Non-polymers4012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.940, 62.270, 89.710
Angle α, β, γ (deg.)90.000, 109.030, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 40698.020 Da / Num. of mol.: 2 / 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.: 2
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
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 2.37 Å3/Da / Density % sol: 48.02 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M TRIS, 25% (W/V) PEG 3350, 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: 1.9→42.896 Å / Num. obs: 60000 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.413 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 7.11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.950.5012.6715150441699.3
1.95-20.4093.3314850427599.4
2-2.060.3583.8214617415799.5
2.06-2.120.3084.4614382407699.7
2.12-2.190.2794.9114030391999.7
2.19-2.270.2445.5213728383699.8
2.27-2.360.2216.0513300369299.6
2.36-2.450.2026.6412803354799.9
2.45-2.560.1827.0812131339299.8
2.56-2.690.1627.911647326599.9
2.69-2.830.1498.2711084311999.7
2.83-30.1299.16103252959100
3-3.210.11510.159414274899.7
3.21-3.470.10410.768518256999.3
3.47-3.80.09411.297568235799.2
3.8-4.250.08911.957156215199.7
4.25-4.910.08312.626622191399.7
4.91-6.010.08212.345768164299.8
6.01-8.50.06812.634459124999.8
8.50.04813.17248671897

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å50.19 Å
Translation2 Å50.19 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→42.896 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.7995 / SU ML: 0.3 / σ(F): 2.04 / Phase error: 27.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2822 3000 5 %
Rwork0.2315 --
obs0.234 59979 99.72 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 15.91 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 56.65 Å2 / Biso mean: 17.2812 Å2 / Biso min: 1.18 Å2
Baniso -1Baniso -2Baniso -3
1--4.9046 Å2-0 Å2-0.8519 Å2
2---0.0528 Å20 Å2
3---4.9573 Å2
Refinement stepCycle: LAST / Resolution: 1.9→42.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5654 0 48 286 5988
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045851
X-RAY DIFFRACTIONf_angle_d0.8057974
X-RAY DIFFRACTIONf_chiral_restr0.054884
X-RAY DIFFRACTIONf_plane_restr0.0031032
X-RAY DIFFRACTIONf_dihedral_angle_d12.0892098
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.93120.33431400.27852668280899
1.9312-1.96450.3191430.262527232866100
1.9645-2.00020.34721410.25312683282499
2.0002-2.03870.32991420.247726892831100
2.0387-2.08030.28551410.251126782819100
2.0803-2.12550.34081420.234827042846100
2.1255-2.17490.28781420.245126932835100
2.1749-2.22930.32941440.236727372881100
2.2293-2.28960.24681420.235526902832100
2.2896-2.3570.30571420.24326912833100
2.357-2.4330.3221420.249527092851100
2.433-2.520.32971430.248827152858100
2.52-2.62090.29931420.239227042846100
2.6209-2.74010.26911440.24727202864100
2.7401-2.88460.30821430.232227292872100
2.8846-3.06530.27391430.243627132856100
3.0653-3.30180.25041430.253227212864100
3.3018-3.6340.30711430.23372718286199
3.634-4.15940.24941440.21952722286699
4.1594-5.2390.25611460.186227682914100
5.239-42.90660.19631480.17822804295299
Refinement TLS params.Method: refined / Origin x: -9.1681 Å / Origin y: 8.8814 Å / Origin z: -21.2224 Å
111213212223313233
T0.0229 Å20.0076 Å2-0.0019 Å2--0.0012 Å2-0.009 Å2---0.0071 Å2
L0.6936 °20.0371 °2-0.0614 °2-0.1118 °20.0134 °2--0.1747 °2
S-0.0097 Å °0.1029 Å °0.0618 Å °-0.0029 Å °0.0101 Å °0.0139 Å °0.0079 Å °-0.0257 Å °0.0012 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 371
3X-RAY DIFFRACTION1ALLC3 - 371

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