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- PDB-4afk: In meso structure of alginate transporter, AlgE, from Pseudomonas... -

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Basic information

Entry
Database: PDB / ID: 4afk
TitleIn meso structure of alginate transporter, AlgE, from Pseudomonas aeruginosa, PAO1
ComponentsALGINATE PRODUCTION PROTEIN ALGE
KeywordsMEMBRANE PROTEIN / OUTER MEMBRANE / LIPIDIC CUBIC PHASE / BETA BARREL
Function / homology
Function and homology information


alginic acid biosynthetic process / cell outer membrane
Similarity search - Function
Porin - #100 / Alginate export domain / Alginate export / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / CITRATE ANION / Alginate production protein AlgE
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 Å
AuthorsTan, J. / Pye, V.E. / Aragao, D. / Caffrey, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: A Conformational Landscape for Alginate Secretion Across the Outer Membrane of Pseudomonas Aeruginosa.
Authors: Tan, J. / Rouse, S.L. / Li, D. / Pye, V.E. / Vogeley, L. / Brinth, A.R. / El Arnaout, T. / Whitney, J.C. / Howell, P.L. / Sansom, M.S.P. / Caffrey, M.
History
DepositionJan 19, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Aug 6, 2014Group: Database references
Revision 1.3Aug 13, 2014Group: Database references
Revision 1.4Sep 30, 2015Group: Database references
Revision 1.5May 22, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.6Mar 29, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary
Category: audit_author / chem_comp ...audit_author / chem_comp / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms ..._audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_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_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
Revision 1.7Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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
A: ALGINATE PRODUCTION PROTEIN ALGE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,59928
Polymers51,2001
Non-polymers6,40027
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.253, 74.416, 115.529
Angle α, β, γ (deg.)90.00, 101.56, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ALGINATE PRODUCTION PROTEIN ALGE


Mass: 51199.520 Da / Num. of mol.: 1 / Fragment: RESIDUES 33-490
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Description: HOLLOWAY COLLECTION / Plasmid: ALGE_PET200/D-TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: P18895

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Non-polymers , 8 types, 269 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#4: Chemical
ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O4
#7: Chemical ChemComp-78N / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL (2R)


Mass: 314.460 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H34O4
#8: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 398.489 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL (PE5): PEG 400 LAURYL DIMETHYLAMINE-N-OXIDE (LDA): SOME ...3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL (PE5): PEG 400 LAURYL DIMETHYLAMINE-N-OXIDE (LDA): SOME LDA MOLECULES HAVE NOT HAD HEAD GROUPS FITTED AS NO ELECTRON DENSITY, ALKANE CHAINS WERE MODELLED WHERE WE WERE UNABLE TO DISTINGUISH BETWEEN LADO AND 7.8 MAG. INCLUSION OF THE TAILS FIT INTO DENSITY AND REDUCES FREE R FACTOR BY 1.2 PERCENT.

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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: 2.36 Å3/Da / Density % sol: 47.96 % / Description: NONE
Crystal growMethod: lipidic cubic phase / pH: 7.5
Details: 0.1 M TRIS-HCL, PH 7.5, 0.1 M SODIUM CITRATE, 18 %(W/V) PEG 400. PROTEIN WAS MIXED WITH 7.8 MAG AT RATIO 1:1 (W:W) TO FORM CUBIC PHASE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 22, 2008
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.9→113.18 Å / Num. obs: 37703 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Biso Wilson estimate: 15.42 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 15.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.9 / % possible all: 84.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RBH

3rbh


Resolution: 1.897→19.77 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 20.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2086 1788 5 %
Rwork0.1633 --
obs0.1656 35580 94.51 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.825 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 23.505 Å2
Baniso -1Baniso -2Baniso -3
1-1.0359 Å20 Å2-1.7468 Å2
2--2.2185 Å20 Å2
3----3.2544 Å2
Refinement stepCycle: LAST / Resolution: 1.897→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3415 0 342 242 3999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013898
X-RAY DIFFRACTIONf_angle_d1.3445199
X-RAY DIFFRACTIONf_dihedral_angle_d19.3791523
X-RAY DIFFRACTIONf_chiral_restr0.099508
X-RAY DIFFRACTIONf_plane_restr0.005669
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8973-1.94860.3114980.21851972X-RAY DIFFRACTION71
1.9486-2.00590.22191290.17392306X-RAY DIFFRACTION86
2.0059-2.07050.21081240.16112526X-RAY DIFFRACTION91
2.0705-2.14440.2281220.15742591X-RAY DIFFRACTION94
2.1444-2.23020.19611300.15332615X-RAY DIFFRACTION95
2.2302-2.33150.22981370.15822647X-RAY DIFFRACTION97
2.3315-2.45430.22971610.15662674X-RAY DIFFRACTION97
2.4543-2.60770.19841380.15472719X-RAY DIFFRACTION98
2.6077-2.80850.21821430.16332688X-RAY DIFFRACTION99
2.8085-3.09020.19171410.16462734X-RAY DIFFRACTION99
3.0902-3.53520.20391600.16012736X-RAY DIFFRACTION100
3.5352-4.44560.19761550.15432770X-RAY DIFFRACTION100
4.4456-19.77120.19421500.17632814X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.29820.0388-0.05080.32970.08090.05120.14730.064-0.0011-0.0113-0.13180.1254-0.12010.0579-0.00850.0106-0.0739-0.02910.0250.00970.07053.6627-8.115432.6708
20.35970.1055-0.10730.2654-0.14650.13830.02360.01170.00350.0486-0.0222-0.005-0.0067-0.002-0.0070.058-0.0023-0.010.05040.00040.056720.1401-14.282333.0461
30.19730.074-0.14010.2544-0.10890.10490.01940.112-0.02150.0175-0.0262-0.03440.1142-0.1331-0.01940.0736-0.02010.00940.1458-0.01650.070824.8815-6.179919.1723
40.55840.0253-0.04310.37550.0740.16180.01740.02050.0147-0.029-0.0070.0145-0.0268-0.01-0.00820.038-0.01050.00450.01740.00710.024416.58857.303628.9381
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 37:118)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 119:232)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 233:313)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 314:490)

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