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- PDB-1oh2: Sucrose-Specific Porin, with Bound Sucrose Molecules -

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Basic information

Entry
Database: PDB / ID: 1oh2
TitleSucrose-Specific Porin, with Bound Sucrose Molecules
Components(Sucrose porin) x 2
KeywordsMEMBRANE PROTEIN / OUTER MEMBRANE PROTEIN / TRANSPORT / SUGAR TRANSPORT / TRANSMEMBRANE
Function / homology
Function and homology information


polysaccharide transport / porin activity / pore complex / carbohydrate transmembrane transporter activity / monoatomic ion transport / cell outer membrane
Similarity search - Function
LamB-type porin N-terminal domain / Maltoporin periplasmic N-terminal extension / Porin, LamB type / Porin, LamB-type / Porin, LamB-type superfamily / LamB porin / Maltoporin; Chain A / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
sucrose / Sucrose porin
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDiederichs, K. / Welte, W.
CitationJournal: To be Published
Title: Sucrose-Specific Porin, with Bound Sucrose Molecules
Authors: Diederichs, K. / Welte, W.
History
DepositionMay 21, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2003Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Nov 21, 2018Group: Data collection / Database references ...Data collection / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / entity_src_nat / struct / struct_ref
Item: _entity.pdbx_description / _entity.src_method ..._entity.pdbx_description / _entity.src_method / _struct.title / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.3May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / 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_conn_angle / struct_asym / struct_conn / struct_conn_type / 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.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "PA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "PA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 20-STRANDED BARREL THIS IS REPRESENTED BY A 21-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "RA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 18-STRANDED BARREL THIS IS REPRESENTED BY A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Sucrose porin
Q: Sucrose porin
R: Sucrose porin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,76512
Polymers135,5913
Non-polymers2,1749
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13420 Å2
ΔGint-129.8 kcal/mol
Surface area53970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.800, 111.800, 147.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Sucrose porin


Mass: 45333.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: scrY / Production host: Escherichia coli (E. coli) / References: UniProt: P22340
#2: Protein Sucrose porin


Mass: 44923.449 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: scrY / Production host: Escherichia coli (E. coli) / References: UniProt: P22340
#3: Polysaccharide
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 6
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
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca

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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: 3.8 Å3/Da / Density % sol: 68 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7.7
Details: PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION USING THE SITTING-DROP METHOD. THE DROP CONTAINED 5-7 MG/ML PROTEIN, 20 MM TRIS/CL AT PH 7.7, 100MM LICL, 20MM MGSO4, 1.2% BETA-D- ...Details: PROTEIN WAS CRYSTALLIZED BY VAPOR DIFFUSION USING THE SITTING-DROP METHOD. THE DROP CONTAINED 5-7 MG/ML PROTEIN, 20 MM TRIS/CL AT PH 7.7, 100MM LICL, 20MM MGSO4, 1.2% BETA-D-OCTYLGLUCOPYRANOSIDE AND 6-9% PEG-2000. THE CONCENTRATION OF PEG IN THE RESERVOIR WAS 12-15%. 2M SUCROSE WAS ADDED TO THE DROP FOR COCRYSTALLIZATION.

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: SCHNEIDER / Wavelength: 1.5418
DetectorType: STOE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→17 Å / Num. obs: 65815 / % possible obs: 80.7 % / Observed criterion σ(I): 0 / Redundancy: 2.74 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 5
Reflection shellResolution: 2.4→3 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2 / % possible all: 84

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AOS

1aos


Resolution: 2.4→100 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
Details: ONLY RESIDUES 71 - 483 OF THE MATURE SEQUENCE COULD BE FITTED INTO THE ELECTRON DENSITY MAP.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 891 2 %RANDOM
Rwork0.207 ---
obs0.207 55335 67.4 %-
Displacement parametersBiso mean: 28.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.31 Å
Luzzati d res low-17 Å
Luzzati sigma a0.43 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9576 0 141 0 9717
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.011
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_deg1.73
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.39
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.521.5
X-RAY DIFFRACTIONx_mcangle_it2.62
X-RAY DIFFRACTIONx_scbond_it2.112
X-RAY DIFFRACTIONx_scangle_it3.112.5
Refine LS restraints NCSRms dev Biso : 1.057 Å2 / Rms dev position: 0.1 Å / Weight Biso : 1 / Weight position: 50
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.058 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3694 41 8.4 %
Rwork0.2945 4826 -
obs--59.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCDSX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM19.IONTOPH19.ION
X-RAY DIFFRACTION4SUC.PARSUC.TOP

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