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- PDB-4gf4: Low pH structure of Pseudomonas putida OprB -

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Basic information

Entry
Database: PDB / ID: 4gf4
TitleLow pH structure of Pseudomonas putida OprB
ComponentsPorin B
KeywordsTRANSPORT PROTEIN / beta-barrel transport outer membrane channel / beta-barrel / carbohydrate transport / bacterial outer membrane
Function / homology
Function and homology information


porin activity / carbohydrate transport / membrane
Similarity search - Function
Carbohydrate-selective porin OprB / Carbohydrate-selective porin OprB / Carbohydrate-selective porin OprB superfamily / : / Carbohydrate-selective porin, OprB family / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Porin, OprB family / :
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.1 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 / Category: software / Item: _software.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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
A: Porin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4105
Polymers49,1841
Non-polymers1,2264
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.037, 122.592, 135.581
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Porin B


Mass: 49184.285 Da / Num. of mol.: 1 / Fragment: unp residues 27-447
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
#2: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
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: 3.34 Å3/Da / Density % sol: 63.16 %
Crystal growTemperature: 293 K / pH: 4
Details: 50 mM sodium-citrate, 0.2 M sodium formate, 35-40% PEG 400 , pH 4.0, VAPOR DIFFUSION, HANGING 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: 3.1→50 Å / Num. obs: 22871 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Rsym value: 0.117 / Net I/σ(I): 21
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 2.4 / % 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: 3.1→19.77 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 29.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.271 1157 10.06 %
Rwork0.214 --
obs0.22 22812 99.2 %
all-22812 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2330 0 68 0 2398
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012447
X-RAY DIFFRACTIONf_angle_d1.4663287
X-RAY DIFFRACTIONf_dihedral_angle_d21.074853
X-RAY DIFFRACTIONf_chiral_restr0.105335
X-RAY DIFFRACTIONf_plane_restr0.006414
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1008-3.1680.42541320.34831160X-RAY DIFFRACTION91
3.168-3.24140.31931370.28881297X-RAY DIFFRACTION100
3.2414-3.32210.35131460.25281322X-RAY DIFFRACTION100
3.3221-3.41150.30351420.24111269X-RAY DIFFRACTION100
3.4115-3.51130.29541410.25161274X-RAY DIFFRACTION99
3.5113-3.6240.30941410.20411282X-RAY DIFFRACTION100
3.624-3.75270.31521430.22311302X-RAY DIFFRACTION100
3.7527-3.90180.25541470.211287X-RAY DIFFRACTION100
3.9018-4.07790.30611460.22131285X-RAY DIFFRACTION100
4.0779-4.29080.26431420.18861292X-RAY DIFFRACTION100
4.2908-4.55660.22511440.1671311X-RAY DIFFRACTION100
4.5566-4.90340.20371480.15891270X-RAY DIFFRACTION100
4.9034-5.38780.22151470.19111296X-RAY DIFFRACTION100
5.3878-6.14680.27041450.211290X-RAY DIFFRACTION100
6.1468-7.66840.29591480.23771305X-RAY DIFFRACTION100
7.6684-19.76560.26011460.23471275X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -3.5832 Å / Origin y: 27.6539 Å / Origin z: 91.5865 Å
111213212223313233
T0.1166 Å20.0267 Å2-0.0068 Å2-0.1184 Å20.0058 Å2--0.1262 Å2
L1.8909 °20.0169 °20.1314 °2-1.1927 °20.459 °2--0.9245 °2
S0.0205 Å °0.1505 Å °-0.2281 Å °-0.0733 Å °-0.0167 Å °-0.0806 Å °-0.0351 Å °0.0491 Å °0.0023 Å °
Refinement TLS groupSelection details: all

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