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- PDB-1a0s: SUCROSE-SPECIFIC PORIN -

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Basic information

Entry
Database: PDB / ID: 1a0s
TitleSUCROSE-SPECIFIC PORIN
ComponentsSUCROSE-SPECIFIC PORIN
KeywordsOUTER MEMBRANE PROTEIN / PORIN
Function / homology
Function and homology information


carbohydrate transmembrane transport / porin activity / pore complex / 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
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MIR / 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 7, 1997Processing site: BNL
Revision 1.0Jun 10, 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 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_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

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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)136,1216
Polymers136,0013
Non-polymers1203
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12120 Å2
ΔGint-135 kcal/mol
Surface area43910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.100, 112.100, 147.000
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, KS 26 / References: UniProt: P22340
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / 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%., 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 %Hexyldimethylamineoxide1drop
71 %btea-D-heptylglucopyranoside1drop
86-9 %PEG20001drop
912-15 %PEG20001reservoir
10100 mMsucrose1drop

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceType: OTHER / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 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: 2.29→17 Å / Num. obs: 130884 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 1.58 % / Biso Wilson estimate: 18.9 Å2 / Rsym value: 0.085 / Net I/σ(I): 8
Reflection shellResolution: 2.29→2.4 Å / Redundancy: 1.53 % / Mean I/σ(I) obs: 3 / Rsym value: 0.301 / % possible all: 65
Reflection
*PLUS
Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 65 % / Rmerge(I) obs: 0.301

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Processing

Software
NameVersionClassification
DAREFImodel building
X-PLOR3.851model building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
DAREFIphasing
X-PLOR3.851phasing
RefinementMethod to determine structure: MIR / Resolution: 2.4→100 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
Details: TWINNING FRACTION 0.011 AS DETERMINED FROM A FINAL SHELXL-96 REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1036 2 %RANDOM
Rwork0.214 ---
obs0.214 63292 78.3 %-
Displacement parametersBiso mean: 27.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-17 Å
Luzzati sigma a0.35 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9606 0 3 330 9939
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_deg1.68
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.37
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.591.5
X-RAY DIFFRACTIONx_mcangle_it2.662
X-RAY DIFFRACTIONx_scbond_it2.312
X-RAY DIFFRACTIONx_scangle_it3.442.5
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms dev Biso : 1.6 Å2 / Weight Biso : 1 / Weight position: 50

Ens-IDDom-IDNCS model detailsRms dev position (Å)
11RESTRAINED0.1
220.09
LS refinement shellResolution: 2.4→2.51 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3116 84 0.83 %
Rwork0.2856 7159 -
obs--71.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCDSX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION3PARAM19.IONTOPH19.ION
Software
*PLUS
Name: X-PLOR / Version: 3.851 / 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_deg28.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.37
LS refinement shell
*PLUS
Rfactor obs: 0.2856

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