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- PDB-1af6: MALTOPORIN SUCROSE COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1af6
TitleMALTOPORIN SUCROSE COMPLEX
ComponentsMALTOPORIN
KeywordsMEMBRANE PROTEIN / SPECIFIC PORIN / BETA BARREL / SUGAR TRANSPORT / SUCROSE
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
sucrose / Maltoporin
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 21, 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_struct_conn_angle / pdbx_validate_close_contact / struct_asym / struct_conn / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 2, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
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)143,40110
Polymers142,2773
Non-polymers1,1247
Water7,098394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13570 Å2
ΔGint-59 kcal/mol
Surface area46820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.660, 211.510, 217.910
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(-0.480908, -0.860876, -0.166193), (0.859298, -0.500433, 0.105705), (-0.174168, -0.091975, 0.980411)39.71622, 47.66848, 4.37183
2given(-0.479529, 0.859932, -0.174839), (-0.861291, -0.499369, -0.093852), (-0.168016, 0.105582, 0.980114)-21.0503, 58.57504, -2.67397

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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 beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose /


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: sucrose
DescriptorTypeProgram
DFrufb2-1DGlcpaGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{[(2+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 394 / 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: 3

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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 0.111MgCl2
411.0-12.5 %(w/w)PEG200011

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.96
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 12, 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 114378 / % possible obs: 99 % / Observed criterion σ(I): 4 / Redundancy: 3.8 % / Biso Wilson estimate: 38.6 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 5.7
Reflection shellResolution: 2.36→2.46 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2 / % possible all: 98.8
Reflection shell
*PLUS
% possible obs: 98.8 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
CCP4model building
PROLSQrefinement
CCP4(ROTAVATA)data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MAL

1mal


Resolution: 2.4→8 Å / Cross valid method: FREE R / σ(F): 0
Details: REFINEMENT WAS PERFORMED USING TIGHT STERICAL RESTRAINTS FOR NCS-RELATED MONOMERS
RfactorNum. reflection% reflectionSelection details
Rfree0.214 -10 %RANDOM
Rwork0.195 ---
obs-112282 99 %-
Displacement parametersBiso mean: 41.5 Å2
Refine analyzeLuzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 2.4→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10050 0 75 396 10521
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0210.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0230.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.3833
X-RAY DIFFRACTIONp_mcangle_it45
X-RAY DIFFRACTIONp_scbond_it6.96
X-RAY DIFFRACTIONp_scangle_it7.28
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor5.77
X-RAY DIFFRACTIONp_staggered_tor17.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS

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