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- PDB-1a0t: SUCROSE-SPECIFIC PORIN, WITH BOUND SUCROSE MOLECULES -

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Basic information

Entry
Database: PDB / ID: 1a0t
TitleSUCROSE-SPECIFIC PORIN, WITH BOUND SUCROSE MOLECULES
ComponentsSUCROSE-SPECIFIC PORIN
KeywordsOUTER MEMBRANE PROTEIN / PORIN
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 / DIFFERENCE FOURIER / Resolution: 2.4 Å
AuthorsDiederichs, K. / Welte, W.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Structure of the sucrose-specific porin ScrY from Salmonella typhimurium and its complex with sucrose.
Authors: Forst, D. / Welte, W. / Wacker, T. / Diederichs, K.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Scry, a Specific Bacterial Outer Membrane Porin
Authors: Forst, D. / Schulein, K. / Wacker, T. / Diederichs, K. / Kreutz, W. / Benz, R. / Welte, W.
History
DepositionDec 8, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Other / Category: diffrn_source / pdbx_database_status
Item: _diffrn_source.type / _pdbx_database_status.process_site
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 2.1Aug 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
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: SUCROSE-SPECIFIC PORIN
Q: SUCROSE-SPECIFIC PORIN
R: SUCROSE-SPECIFIC PORIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,17512
Polymers136,0013
Non-polymers2,1749
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15250 Å2
ΔGint-116 kcal/mol
Surface area43200 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.49839, 0.864212, 0.06888), (-0.866499, -0.499125, -0.007322), (0.028052, -0.063334, 0.997598)-54.441, -31.931, 1.0074
2given(-0.499843, -0.865649, 0.02843), (0.863846, -0.50064, -0.055946), (0.062663, -0.003405, 0.998029)-54.9001, 31.273, 2.2337

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Components

#1: Protein SUCROSE-SPECIFIC PORIN


Mass: 45333.668 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Cellular location: OUTER MEMBRANE / Gene: SCRY / Plasmid: PSO112 / Cellular location (production host): OUTER MEMBRANE / Production host: Escherichia coli (E. coli) / Strain (production host): K-12 / Variant (production host): KS 26 / References: UniProt: P22340
#2: 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
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 330 / 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: 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., vapor diffusion - sitting drop
Crystal grow
*PLUS
Temperature: 17 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-7 mg/mlprotein1drop
220 mMTris-Cl1drop
3100 mM1dropLiCl
420 mM1dropMgSO4
51.2 %beta-D-octylglucopyranoside1drop
61 %C6DAO1drop
71 %beta-D-heptylglucopyranoside1drop
86-9 %PEG20001drop
9100 mMsucrose1drop
1012-15 %PEG20001reservoir

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceType: OTHER / Wavelength: 1.5418
DetectorType: STOE / Detector: DIFFRACTOMETER / Date: Apr 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / 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 / Rsym value: 0.155 / Net I/σ(I): 5
Reflection shellResolution: 2.4→3 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2 / Rsym value: 0.524 / % possible all: 84
Reflection
*PLUS
Rmerge(I) obs: 0.161

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: SUCROSE PORIN (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
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. atoms9606 0 141 330 10077
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 NCS

Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0.1 Å / Weight Biso : 1 / Weight position: 50

Ens-IDDom-IDNCS model detailsRms dev Biso (Å2)
11RESTRAINTS0.562
221.057
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
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.39

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