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- PDB-1mpq: MALTOPORIN TREHALOSE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1mpq
TitleMALTOPORIN TREHALOSE COMPLEX
ComponentsMALTOPORIN
KeywordsMEMBRANE PROTEIN / SPECIFIC PORIN / BETA BARREL / SUGAR TRANSPORT
Function / homology
Function and homology information


maltodextrin transmembrane transporter activity / maltose transporting porin activity / polysaccharide transport / porin activity / maltodextrin transmembrane transport / pore complex / carbohydrate transmembrane transporter activity / monoatomic ion transport / cell outer membrane / virus receptor activity / DNA damage response
Similarity search - Function
Porin, LamB type / Maltoporin / Porin, LamB-type / Porin, LamB-type superfamily / LamB porin / Maltoporin; Chain A / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
trehalose / Maltoporin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDutzler, R. / Schirmer, T.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Channel specificity: structural basis for sugar discrimination and differential flux rates in maltoporin.
Authors: Wang, Y.F. / Dutzler, R. / Rizkallah, P.J. / Rosenbusch, J.P. / Schirmer, T.
#1: Journal: Structure / Year: 1996
Title: Crystal Structures of Various Maltooligosaccharides Bound to Maltoporin Reveal a Specific Sugar Translocation Pathway
Authors: Dutzler, R. / Wang, Y.F. / Rizkallah, P. / Rosenbusch, J.P. / Schirmer, T.
#2: Journal: Science / Year: 1995
Title: Structural Basis for Sugar Translocation Through Maltoporin Channels at 3.1 A Resolution
Authors: Schirmer, T. / Keller, T.A. / Wang, Y.F. / Rosenbusch, J.P.
History
DepositionMar 24, 1997Processing site: BNL
Revision 1.0Mar 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _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
Revision 2.1Aug 9, 2023Group: Advisory / Database references ...Advisory / Database references / Refinement description / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
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: MALTOPORIN
B: MALTOPORIN
C: MALTOPORIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,3046
Polymers142,2773
Non-polymers1,0273
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13190 Å2
ΔGint-61 kcal/mol
Surface area47000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.000, 212.200, 218.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.480296, -0.860981, -0.167412), (0.859643, -0.499977, 0.105056), (-0.174153, -0.093456, 0.980274)39.89709, 47.85519, 4.41551
2given(-0.480267, 0.859631, -0.174291), (-0.860975, -0.499977, -0.093512), (-0.167527, 0.10515, 0.980244)-21.20666, 58.6898, -2.67924

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Components

#1: Protein MALTOPORIN / / LAMB


Mass: 47425.785 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Cellular location: OUTER MEMBRANE / Gene: LAMB / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P02943
#2: Polysaccharide alpha-D-glucopyranose-(1-1)-alpha-D-glucopyranose / trehalose /


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: trehalose
DescriptorTypeProgram
DGlcpa1-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a1-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(1+1)][a-D-Glcp]{}}LINUCSPDB-CARE
Nonpolymer detailsGLC 1 OF TREHALOSE WAS DISORDERED AND THUS MODELED STEREOCHEMICALLY. A SINGLE GROUP B-FACTOR WAS ...GLC 1 OF TREHALOSE WAS DISORDERED AND THUS MODELED STEREOCHEMICALLY. A SINGLE GROUP B-FACTOR WAS REFINED FOR GLC2 ATOMIC B-FACTORS OF THE PROTEIN WERE TAKEN FROM THE MALTOPORIN-SUCROSE MODEL (2.4A); ONLY THE OVERALL B-FACTOR WAS REFINED.

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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: 5.29 Å3/Da / Density % sol: 75 %
Crystal growpH: 7 / Details: pH 7.
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.4 %(w/w)beta-D-decylmaltoside11
220 mMHEPES11
30.1 M11MgCl2
411.0-12.5 %(w/w)PEG200011

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-20 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 12, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 59057 / % possible obs: 97.7 % / Observed criterion σ(I): 4 / Redundancy: 3.3 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.078
Reflection shellResolution: 3→3.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.5 / % possible all: 93.2
Reflection shell
*PLUS
% possible obs: 93.2 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
CCP4(ROTAVATA)data scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MAL

1mal


Resolution: 3→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.241 -10 %RANDOM
Rwork0.218 ---
obs0.218 59021 97.6 %-
Displacement parametersBiso mean: 21.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.6493 Å20 Å20 Å2
2--2.9522 Å20 Å2
3----4.6015 Å2
Refinement stepCycle: LAST / Resolution: 3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3350 0 23 0 3373
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.15
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.76
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: STRICT NCS CONSTRAINTS
LS refinement shellResolution: 3→3.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 -8 %
Rwork0.41 2209 -
obs--86.25 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH3.CHO
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.76

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