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- PDB-2mpr: MALTOPORIN FROM SALMONELLA TYPHIMURIUM -

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Basic information

Entry
Database: PDB / ID: 2mpr
TitleMALTOPORIN FROM SALMONELLA TYPHIMURIUM
ComponentsMALTOPORIN
KeywordsOUTER MEMBRANE PROTEIN / OLIGOSACCHARIDE BINDING / SUGAR TRANSPORT / PHAGE RECOGNITION
Function / homology
Function and homology information


maltodextrin transmembrane transporter activity / maltose transporting porin activity / polysaccharide transport / porin activity / pore complex / carbohydrate transmembrane transporter activity / monoatomic ion transport / cell outer membrane
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-maltotriose / Maltoporin
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMeyer, J.E.W. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 1997
Title: Structure of maltoporin from Salmonella typhimurium ligated with a nitrophenyl-maltotrioside.
Authors: Meyer, J.E. / Hofnung, M. / Schulz, G.E.
History
DepositionFeb 7, 1997Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.type
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _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 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
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)145,7477
Polymers144,1943
Non-polymers1,5534
Water10,088560
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14870 Å2
ΔGint-45 kcal/mol
Surface area46240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.500, 211.800, 184.300
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(-0.487541, -0.864344, -0.123338), (0.863609, -0.498178, 0.077447), (-0.128385, -0.068757, 0.989338)65.33897, 99.9594, 5.30578
2given(-0.486621, -0.864788, -0.123859), (0.864061, -0.497347, 0.077743), (-0.128832, -0.06919, 0.98925)65.39, 99.9, 5.33
3given(-0.489234, 0.862345, -0.130424), (-0.862697, -0.500449, -0.072835), (-0.12808, 0.076883, 0.988779)-53.57, 107.05, -4.72
4given(-0.488529, 0.862765, -0.130288), (-0.863157, -0.499701, -0.072512), (-0.127666, 0.077035, 0.988821)-53.59, 107, -4.72
5given(-0.478397, -0.869753, -0.121105), (0.869924, -0.488216, 0.06984), (-0.119869, -0.071941, 0.99018)65.45, 99.95, 5.39
6given(-0.494168, 0.859698, -0.129292), (-0.860255, -0.505026, -0.070072), (-0.125536, 0.076597, 0.989128)-53.49, 107.11, -4.73

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Components

#1: Protein MALTOPORIN / LAM-B / MAL-L


Mass: 48064.535 Da / Num. of mol.: 3 / Fragment: MATURE PROTEIN, SIGNAL SEQUENCE CLEAVED OFF / Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria) / Cellular location: OUTER MEMBRANE / Strain: SL3749 / References: UniProt: P26466
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 560 / 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: 1

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Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71 %
Crystal growMethod: vapor diffusion, hanging drop
Details: MALTOPORIN WAS CRYSTALLIZED BY HANGING-DROP METHOD. DROP: 5-8 MG/ML PROTEIN, 0.3% C8E4, 0.8% C6DAO, 1 MM CACL2, 1MM MGCL2, 14-18% PEG 1500, 0.02% NAN3 RESERVOIR: 28-32% PEG 1500, vapor diffusion - hanging drop
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-8 mg/mlprotein1drop
20.3 %n-octyltetraoxyethylene1drop
30.8 %n-hexyldimethylaminoxide1drop
41 mM1dropMgCl2
51 mM1dropCaCl2
614-18 %PEG15001drop
70.02 %1dropNaN3
828-32 %PEG15001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Sep 4, 1995
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→25 Å / Num. obs: 90607 / Redundancy: 3.1 % / Biso Wilson estimate: 36 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 4.3 / Rsym value: 0.167 / % possible all: 62.4
Reflection
*PLUS
% possible obs: 88 % / Num. measured all: 278202
Reflection shell
*PLUS
% possible obs: 62 % / Rmerge(I) obs: 0.35

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Processing

Software
NameClassification
XDSdata scaling
XSCALEdata scaling
AMoREphasing
RAVEmodel building
X-PLORmodel building
X-PLORrefinement
XDSdata reduction
RAVEphasing
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MPR

1mpr


Resolution: 2.4→10 Å / Rfactor Rfree error: 0.0034 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED
Cross valid method: THROUGHOUT, EXCEPT FOR VERY LAST ROUND (REFINEMENT AGAINST ALL REFLECTIONS)
σ(F): 0
Details: THE ENTRY PRESENTS THE REFINED STRUCTURE CONTAINING 1 MALTOTRIOSE PER MONOMER. ALL SIDE CHAIN ATOMS WITHOUT DENSITY WERE ASSIGNED ZERO OCCUPANCY. B-VALUES OF WILSON PLOT WAS CALCULATED WITH ...Details: THE ENTRY PRESENTS THE REFINED STRUCTURE CONTAINING 1 MALTOTRIOSE PER MONOMER. ALL SIDE CHAIN ATOMS WITHOUT DENSITY WERE ASSIGNED ZERO OCCUPANCY. B-VALUES OF WILSON PLOT WAS CALCULATED WITH THE CCP4 PROGRAM WILSON.
RfactorNum. reflection% reflectionSelection details
Rfree0.222 4219 5.1 %RANDOM
Rwork0.191 ---
obs0.191 82445 88.1 %-
Displacement parametersBiso mean: 26.7 Å2
Refine analyzeLuzzati d res low obs: 3.53 Å / Luzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.4→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10056 0 103 560 10719
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.16
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 1.7 Å2 / Rms dev position: 0.2 Å / Weight Biso : 0.2 / Weight position: 100
LS refinement shellResolution: 2.4→2.48 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.293 307 5.4 %
Rwork0.271 5737 -
obs--62 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 27 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.16
LS refinement shell
*PLUS
Rfactor obs: 0.271

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