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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 / homologyPorin, LamB-type / Maltoporin / Porin, LamB-type superfamily / LamB porin / maltodextrin transmembrane transporter activity / maltose transporting porin activity / integral component of cell outer membrane / porin activity / maltodextrin transport / pore complex ...Porin, LamB-type / Maltoporin / Porin, LamB-type superfamily / LamB porin / maltodextrin transmembrane transporter activity / maltose transporting porin activity / integral component of cell outer membrane / porin activity / maltodextrin transport / pore complex / ion transport / cell outer membrane / virus receptor activity / cellular response to DNA damage stimulus / Maltoporin
Function and homology information
Specimen sourceEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.4 Å resolution
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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 21, 1997 / Release: Mar 25, 1998
RevisionDateData content typeGroupProviderType
1.0Mar 25, 1998Structure modelrepositoryInitial release
1.1Mar 3, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MALTOPORIN
B: MALTOPORIN
C: MALTOPORIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,45613
Polyers142,2773
Non-polymers1,17810
Water7,098394
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)13570
ΔGint (kcal/M)-59
Surface area (Å2)46820
MethodPISA
Unit cell
γ
α
β
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-MC 2 2 21

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Components

#1: Protein/peptide MALTOPORIN / / LAMB


Mass: 47425.785 Da / Num. of mol.: 3 / Source: (gene. exp.) Escherichia coli (E. coli) / Genus: Escherichia / Cellular location: OUTER MEMBRANE / Gene: LAMB / Genus (production host): Escherichia / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P02943
#2: Chemical ChemComp-GLC / ALPHA-D-GLUCOSE


Mass: 180.156 Da / Num. of mol.: 3 / Formula: C6H12O6 / Glucose
#3: Chemical ChemComp-FRU / FRUCTOSE


Mass: 180.156 Da / Num. of mol.: 3 / Formula: C6H12O6 / Fructose
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Formula: Mg / Magnesium
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 394 / Formula: H2O / Water

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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 percent sol: 75 %
Crystal growpH: 7 / Details: pH 7.
Crystal grow
*PLUS
Method: unknown
components of the solutions
*PLUS
IDConcCommon 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 kelvins
SourceSource: SYNCHROTRON / Type: SRS BEAMLINE PX9.6 / Synchrotron site: SRS / Beamline: PX9.6 / Wavelength: 0.96
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Collection date: May 12, 1995
RadiationMonochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionB iso Wilson estimate: 38.6 Å2 / D resolution high: 2.4 Å / D resolution low: 2 Å / Number obs: 114378 / Observed criterion sigma I: 4 / Rmerge I obs: 0.065 / NetI over sigmaI: 5.7 / Redundancy: 3.8 % / Percent possible obs: 99
Reflection shellRmerge I obs: 0.35 / Highest resolution: 2.36 Å / Lowest resolution: 2.46 Å / MeanI over sigI obs: 2 / Redundancy: 3.9 % / Percent possible all: 98.8
Reflection shell
*PLUS
Percent possible obs: 98.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
CCP4model building
PROLSQrefinement
CCP4(ROTAVATA)data scaling
CCP4phasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MAL
Details: REFINEMENT WAS PERFORMED USING TIGHT STERICAL RESTRAINTS FOR NCS-RELATED MONOMERS
R Free selection details: RANDOM / Cross valid method: FREE R / Sigma F: 0
Displacement parametersB iso mean: 41.5 Å2
Least-squares processR factor R free: 0.214 / R factor R work: 0.195 / Highest resolution: 2.4 Å / Lowest resolution: 8 Å / Number reflection obs: 112282 / Percent reflection R free: 1 / Percent reflection obs: 99
Refine analyzeLuzzati d res low obs: 8 Å
Refine hist #LASTHighest resolution: 2.4 Å / Lowest resolution: 8 Å
Number of atoms included #LASTProtein: 10050 / Nucleic acid: 0 / Ligand: 75 / Solvent: 396 / Total: 10521
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.020
X-RAY DIFFRACTIONp_angle_d0.0210.030
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0230.050
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.3833.0
X-RAY DIFFRACTIONp_mcangle_it4.05.0
X-RAY DIFFRACTIONp_scbond_it6.96.0
X-RAY DIFFRACTIONp_scangle_it7.28.0
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_tor5.77.0
X-RAY DIFFRACTIONp_staggered_tor17.715.0
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Least-squares process
*PLUS
R factor obs: 0.195

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