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- PDB-1mpr: MALTOPORIN FROM SALMONELLA TYPHIMURIUM -

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Basic information

Entry
Database: PDB / ID: 1mpr
TitleMALTOPORIN FROM SALMONELLA TYPHIMURIUM
ComponentsMALTOPORIN
KeywordsMEMBRANE PROTEIN / SUGAR TRANSPORT / SPECIFIC PORIN / BETA BARREL
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
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionDec 18, 1996Processing site: BNL
Revision 1.0Mar 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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.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.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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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)144,2344
Polymers144,1943
Non-polymers401
Water8,215456
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-97 kcal/mol
Surface area47060 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(-0.485188, -0.86523, -0.126372), (0.864567, -0.496314, 0.078721), (-0.130832, -0.071063, 0.988854)65.469, 99.768, 5.469
2given(-0.488925, 0.862163, -0.132768), (-0.862384, -0.500635, -0.075227), (-0.131326, 0.077716, 0.988288)-53.397, 107.155, -4.741
DetailsTHE FOLLOWING TRANSFORMATION WILL TRANSFORM THE WATERS OF CHAIN A INTO THE WATERS OF CHAIN B. MTRIX1 -0.485848 -0.865005 -0.125370 65.39400 MTRIX2 0.864287 -0.496828 0.078542 99.80500 MTRIX3 -0.130227 -0.070196 0.988996 5.42100 THE FOLLOWING TRANSFORMATION WILL TRANSFORM THE WATERS OF CHAIN A INTO THE WATERS OF CHAIN C. MTRIX1 -0.488651 0.862290 -0.132950 -53.38000 MTRIX2 -0.862650 -0.500312 -0.074311 107.08700 MTRIX3 -0.130594 0.078377 0.988333 -4.78000

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Components

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


Mass: 48064.535 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Salmonella typhimurium (bacteria) / Cellular location: OUTER MEMBRANE / Strain: SL3749 / References: UniProt: P26466
#2: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O
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: 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 %C8E41drop
30.8 %C6DAO(Fluka)1drop
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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 14, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 59257 / % possible obs: 95 % / Redundancy: 2.9 % / Biso Wilson estimate: 45 Å2 / Rsym value: 0.072 / Net I/σ(I): 7.1
Reflection shellResolution: 2.77→2.84 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.259 / % possible all: 91.4
Reflection
*PLUS
Num. measured all: 171366 / Rmerge(I) obs: 0.072
Reflection shell
*PLUS
% possible obs: 91.4 % / Rmerge(I) obs: 0.259

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Processing

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

1mal


Resolution: 2.8→10 Å / Rfactor Rfree error: 0.0028 / 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: 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
Rfree0.211 5612 10 %RANDOM
Rwork0.183 ---
obs0.183 55677 94.8 %-
Displacement parametersBiso mean: 21.1 Å2
Refine analyzeLuzzati d res low obs: 3.56 Å / Luzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10059 0 1 456 10516
Refine LS restraints
Refine-IDTypeDev ideal
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_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.2
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
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev Biso : 2 Å2 / Rms dev position: 0.2 Å / Weight Biso : 0.2 / Weight position: 100
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.264 518 9.7 %
Rwork0.238 5320 -
obs--91.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
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_deg27.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.2

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