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- PDB-1mpm: MALTOPORIN MALTOSE COMPLEX -

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Basic information

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


maltose transmembrane transporter activity / maltose transmembrane transport / maltodextrin transmembrane transporter activity / maltose transporting porin activity / outer membrane protein complex / polysaccharide transport / porin activity / pore complex / carbohydrate transmembrane transporter activity / maltodextrin transmembrane transport ...maltose transmembrane transporter activity / maltose transmembrane transport / maltodextrin transmembrane transporter activity / maltose transporting porin activity / outer membrane protein complex / polysaccharide transport / porin activity / pore complex / carbohydrate transmembrane transporter activity / maltodextrin transmembrane transport / 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
beta-maltose / Maltoporin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsDutzler, R. / Schirmer, T.
Citation
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.J. / Rosenbusch, J.P. / Schirmer, T.
#1: 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
DepositionJan 11, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 25, 2015Group: Database references
Revision 1.4Mar 15, 2017Group: Derived calculations
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_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)144,40412
Polymers142,2773
Non-polymers2,1279
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15690 Å2
ΔGint-35 kcal/mol
Surface area46130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.800, 211.700, 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(-0.481059, -0.861461, -0.162687), (0.859592, -0.499954, 0.105583), (-0.172291, -0.089053, 0.981012)39.7, 47.77, 4.22
2given(-0.481059, 0.859592, -0.172291), (-0.861461, -0.499954, -0.089053), (-0.162687, 0.105583, 0.981012)-21.24, 58.46, -2.73
DetailsTHE ASYMMETRIC UNIT CONTAINS THREE MONOMERS A, B, AND C. CHAINS B AND C OF THE ENTRY HAVE BEEN GENERATED BY THE PDB TO PROVIDE THE OTHER TWO SUBUNITS OF THE MOLECULAR THREE-FOLD TRIMER.

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Components

#1: Protein MALTOPORIN / LAMB


Mass: 47425.785 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P02943
#2: Polysaccharide
alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsMALTOSE CONSISTS OF TWO ALPHA-1-4 LINKED GLUCOSYL RESIDUES. THE GLUCOSYL RESIDUES OF THE TWO ...MALTOSE CONSISTS OF TWO ALPHA-1-4 LINKED GLUCOSYL RESIDUES. THE GLUCOSYL RESIDUES OF THE TWO MALTOSE MOLECULES ARE RESIDUES 431 - 432 AND 441 - 442 RESPECTIVELY. THE TWO MOLECULES OVERLAP AND REPRESENT ALTERNATIVE BINDING MODES. AN OCCUPANCY OF 0.5 HAS BEEN ASSIGNED TO THE TWO MALTOSE MOLECULES. THE TWO MALTOSE POSITIONS ARE SLIGHTLY OVERLAPPING. INTERACTION BETWEEN THE TWO MALTOSE MOLECULES WAS EXCLUDED DURING REFINEMENT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity % 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: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.96
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 9, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 81651 / % possible obs: 89.2 % / Observed criterion σ(I): 4 / Redundancy: 3.6 % / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.7 Å / % possible obs: 90.9 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.345

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementResolution: 2.6→8 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.243 -10 %
Rwork0.226 --
obs0.226 79015 89.5 %
Displacement parametersBiso mean: 34.3 Å2
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10050 0 141 471 10662
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
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_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it3
X-RAY DIFFRACTIONx_scbond_it3
X-RAY DIFFRACTIONx_scangle_it4
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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