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- PDB-1mal: STRUCTURAL BASIS FOR SUGAR TRANSLOCATION THROUGH MALTOPORIN CHANN... -

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Basic information

Entry
Database: PDB / ID: 1mal
TitleSTRUCTURAL BASIS FOR SUGAR TRANSLOCATION THROUGH MALTOPORIN CHANNELS AT 3.1 ANGSTROMS RESOLUTION
ComponentsMALTOPORIN
KeywordsOUTER MEMBRANE PROTEIN
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3.1 Å
AuthorsSchirmer, T.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1990
Title: Crystallization and Preliminary X-Ray Characterization of Maltoporin from E.Coli
Authors: Stauffer, K.A. / Page, M.P.G. / Hardmeyer, A. / Keller, T.A. / Pauptit, R.A.
History
DepositionNov 24, 1994Processing site: BNL
Revision 1.0Dec 31, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700SHEET THE SHEET PRESENTED AS *A* ON SHEET RECORDS BELOW IS ACTUALLY A EIGHTEEN-STRANDED BETA-BARREL. ...SHEET THE SHEET PRESENTED AS *A* ON SHEET RECORDS BELOW IS ACTUALLY A EIGHTEEN-STRANDED BETA-BARREL. THIS IS REPRESENTED BY A NINETEEN-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THERE IS A BETA-BULGE IN STRAND 6 (RESIDUES 131 - 132) AND IN STRAND 8 (RESIDUES 177 - 178).

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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


Theoretical massNumber of molelcules
Total (without water)142,2773
Polymers142,2773
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11140 Å2
ΔGint-84 kcal/mol
Surface area49200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.890, 214.790, 220.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: CIS PROLINE - PRO 361
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.4824, -0.861598, -0.15782), (0.860309, -0.500011, 0.099693), (-0.164794, -0.087703, 0.982397)39.92, 48.79, 4.15
2given(-0.4824, 0.860309, -0.164794), (-0.861598, -0.500011, -0.087703), (-0.15782, 0.099693, 0.982397)-22.03, 59.16, -2.64

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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) / Organelle: OUTER MEMBRANE / References: UniProt: P02943
Has protein modificationY

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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: 5.48 Å3/Da / Density % sol: 77.56 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlLamB1drop
23.6 %(w/v)PEG40001drop
30.25 %(w/v)C8-POE1drop
40.25 %(w/v)beta-OG1drop
525.2 %(w/v)PEG40001reservoir
60.7 M1reservoirNaCl
70.14 Msodium phosphate1reservoir
83 mM1reservoirNaN3

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Data collection

DetectorDate: Jan 7, 1994
RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.1→8 Å / Num. obs: 51039 / % possible obs: 95.5 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.088
Reflection
*PLUS
Rmerge(I) obs: 0.088

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Processing

Software
NameClassification
MOSFLMdata reduction
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 3.1→8 Å / σ(F): 0
Details: ATOMS THAT ARE NOT DEFINED BY ELECTRON-DENSITY HAVE BEEN ASSIGNED AN OCCUPANCY OF 0.0. RESIDUE ASP 78 IS CLOSE TO THE LOCAL THREE-FOLD AXIS; INTERACTIONS WITH ITS LOCAL SYMMETRY MATES ARE ...Details: ATOMS THAT ARE NOT DEFINED BY ELECTRON-DENSITY HAVE BEEN ASSIGNED AN OCCUPANCY OF 0.0. RESIDUE ASP 78 IS CLOSE TO THE LOCAL THREE-FOLD AXIS; INTERACTIONS WITH ITS LOCAL SYMMETRY MATES ARE MEDIATED BY AN UNMODELED ATOM OR MOLECULE (PROBABLY A CATION) THAT IS LOCATED ON THE THREE-FOLD AXIS AS JUDGED BY THE APPARENT STRONG ELECTRON DENSITY.
RfactorNum. reflection% reflection
Rfree0.24 -10 %
Rwork0.217 --
obs0.217 51039 95.5 %
Displacement parametersBiso mean: 34.3 Å2
Refinement stepCycle: LAST / Resolution: 3.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10050 0 0 0 10050
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_deg2.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.82
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
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_deg28.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.82

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