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- PDB-4gey: High pH structure of Pseudomonas putida OprB -

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Basic information

Entry
Database: PDB / ID: 4gey
TitleHigh pH structure of Pseudomonas putida OprB
ComponentsPorin B
KeywordsTRANSPORT PROTEIN / beta-barrel / outer membrane channel / carbohydrate transport
Function / homology
Function and homology information


porin activity / carbohydrate transport / membrane
Similarity search - Function
Carbohydrate-selective porin OprB / Carbohydrate-selective porin OprB superfamily / : / Carbohydrate-selective porin, OprB family
Similarity search - Domain/homology
beta-D-glucopyranose / PHOSPHATE ION / Porin, OprB family / :
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
Authorsvan den Berg, B.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis for outer membrane sugar uptake in pseudomonads.
Authors: van den Berg, B.
History
DepositionAug 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Jan 2, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name / _software.name
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Porin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,71115
Polymers49,0541
Non-polymers4,65714
Water84747
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.343, 88.343, 177.706
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Porin B


Mass: 49054.418 Da / Num. of mol.: 1 / Fragment: unp residues 27-447 / Mutation: L246(MSE), L248(MSE)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: Pseudomonas putida F1 / Gene: PPUBIRD1_1069 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: E4R6F8, UniProt: A5VZA8*PLUS

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Sugars , 2 types, 5 molecules

#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 3 types, 56 molecules

#3: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 4.08 Å3/Da / Density % sol: 69.86 %
Crystal growTemperature: 293 K / pH: 8.5
Details: 50 mM Tris-HCl, 0.2 M Sodium-phosphate, 10% PEG 4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.97
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 19, 2012
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 22711 / % possible obs: 99.9 % / Observed criterion σ(I): -3
Reflection shellResolution: 2.7→2.75 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→19.98 Å / SU ML: 0.29 / σ(F): 0 / Phase error: 23.09 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.239 1968 8.86 %
Rwork0.188 --
obs0.193 22209 98.2 %
all-22209 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3309 0 241 47 3597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083639
X-RAY DIFFRACTIONf_angle_d1.3344902
X-RAY DIFFRACTIONf_dihedral_angle_d20.6721510
X-RAY DIFFRACTIONf_chiral_restr0.09467
X-RAY DIFFRACTIONf_plane_restr0.007614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7029-2.77030.29011360.21541407X-RAY DIFFRACTION95
2.7703-2.8450.29941340.22581378X-RAY DIFFRACTION96
2.845-2.92850.29291340.20991400X-RAY DIFFRACTION97
2.9285-3.02270.28011350.21651382X-RAY DIFFRACTION96
3.0227-3.13030.26471370.20061420X-RAY DIFFRACTION97
3.1303-3.25520.28321390.20191436X-RAY DIFFRACTION98
3.2552-3.40260.27741380.20021434X-RAY DIFFRACTION98
3.4026-3.5810.23021430.18921422X-RAY DIFFRACTION99
3.581-3.8040.22641410.17361452X-RAY DIFFRACTION99
3.804-4.09530.22381420.17921452X-RAY DIFFRACTION99
4.0953-4.50320.19491410.1671500X-RAY DIFFRACTION100
4.5032-5.14510.21541490.15131473X-RAY DIFFRACTION100
5.1451-6.44590.22941460.1911500X-RAY DIFFRACTION100
6.4459-19.97680.24021530.20941585X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 25.3753 Å / Origin y: 40.1975 Å / Origin z: 66.262 Å
111213212223313233
T0.1358 Å20.0213 Å2-0.0144 Å2-0.3714 Å20.0034 Å2--0.2412 Å2
L1.0236 °20.2289 °20.292 °2-1.2216 °20.4445 °2--1.0723 °2
S0.0469 Å °-0.0425 Å °-0.1072 Å °0.0209 Å °-0.009 Å °0.0342 Å °0.0487 Å °-0.0782 Å °-0.0428 Å °
Refinement TLS groupSelection details: all

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