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- PDB-4b61: In meso structure of alginate transporter, AlgE, from Pseudomoas ... -

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Entry
Database: PDB / ID: 4b61
TitleIn meso structure of alginate transporter, AlgE, from Pseudomoas aeruginosa, PAO1. Crystal form 3.
ComponentsALGINATE PRODUCTION PROTEIN ALGE
KeywordsMEMBRANE PROTEIN / OUTER MEMBRANE / IN MESO CRYSTALLISATION / LIPIDIC CUBIC PHASE
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 / ACETATE ION / COPPER (II) ION / Alginate production protein AlgE
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.402 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
DepositionAug 8, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 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 1.5Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
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 / database_2 ...audit_author / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI ..._audit_author.identifier_ORCID / _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_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_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. THE SHEETS PRESENTED AS "BA" 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
B: ALGINATE PRODUCTION PROTEIN ALGE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,51333
Polymers102,3992
Non-polymers8,11431
Water3,675204
1
A: ALGINATE PRODUCTION PROTEIN ALGE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,72719
Polymers51,2001
Non-polymers4,52818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALGINATE PRODUCTION PROTEIN ALGE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,78614
Polymers51,2001
Non-polymers3,58613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.672, 77.463, 240.290
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9796, 0.1544, -0.1289), (-0.1551, 0.9879, 0.004626), (0.1281, 0.01547, 0.9916)
Vector: -35.98, -38.46, -0.2397)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ALGINATE PRODUCTION PROTEIN ALGE / ALGE


Mass: 51199.520 Da / Num. of mol.: 2 / Fragment: RESIDUES 33-490
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PAO1 (bacteria) / 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 , 7 types, 235 molecules

#2: Chemical...
ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C18H34O4
#3: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE / Lauryldimethylamine oxide


Mass: 229.402 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#6: Chemical ChemComp-78N / (2R)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL (2R)


Mass: 314.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O4
#7: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE (78M): BOTH 2S AND 2R PRESENT. LIPIDS WITHOUT ...(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE (78M): BOTH 2S AND 2R PRESENT. LIPIDS WITHOUT HEADGROUP SEEN MODELLED AS ALKYL CHAINS - BUT THESE COULD BE DETERGENT.
Sequence detailsSTRUCTURE CONTAINS FOLLOWING RESIDUES 38-105, 117-471, 475- 490 DATABASE PSEUDOMONAS GENOME ...STRUCTURE CONTAINS FOLLOWING RESIDUES 38-105, 117-471, 475- 490 DATABASE PSEUDOMONAS GENOME DATABASE (V2) STRUCTURE CONTAINS FOLLOWING RESIDUES 39-105, 116-440, 454- 490 DATABASE PSEUDOMONAS GENOME DATABASE (V2)

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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: 2.81 Å3/Da / Density % sol: 56.26 % / Description: NONE
Crystal growMethod: lipidic cubic phase / pH: 6.5
Details: 0.1 M SODIUM CACODYLATE, PH 6.5, 1.1 M SODIUM ACETATE IN SOLUTION; PROTEIN RECONSTITUTED IN LIPIDIC CUBIC PHASE USING 7.8 MAG AS THE HOSTING LIPID.

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 17, 2009
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: 2.4→55.64 Å / Num. obs: 45680 / % possible obs: 98.6 % / Observed criterion σ(I): 1.8 / Redundancy: 9.3 % / Biso Wilson estimate: 35.72 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3RBH

3rbh


Resolution: 2.402→48.865 Å / SU ML: 0.3 / σ(F): 1.35 / Phase error: 24.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2436 2299 5 %
Rwork0.2205 --
obs0.2217 45596 99.25 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.62 Å2 / ksol: 0.351 e/Å3
Displacement parametersBiso mean: 40.72 Å2
Baniso -1Baniso -2Baniso -3
1-11.17 Å20 Å20 Å2
2---5 Å20 Å2
3----6 Å2
Refinement stepCycle: LAST / Resolution: 2.402→48.865 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6903 0 333 204 7440
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0197479
X-RAY DIFFRACTIONf_angle_d1.10910050
X-RAY DIFFRACTIONf_dihedral_angle_d15.2982769
X-RAY DIFFRACTIONf_chiral_restr0.081999
X-RAY DIFFRACTIONf_plane_restr0.0041322
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.402-2.45420.3411550.30622667X-RAY DIFFRACTION100
2.4542-2.51130.3271350.28852688X-RAY DIFFRACTION100
2.5113-2.57410.31811250.27172714X-RAY DIFFRACTION100
2.5741-2.64370.29871510.26412655X-RAY DIFFRACTION100
2.6437-2.72150.31371420.25822664X-RAY DIFFRACTION100
2.7215-2.80940.28191460.24352712X-RAY DIFFRACTION100
2.8094-2.90970.28991440.23622687X-RAY DIFFRACTION100
2.9097-3.02620.26491390.24062691X-RAY DIFFRACTION100
3.0262-3.16390.27871350.22212686X-RAY DIFFRACTION99
3.1639-3.33070.23091500.20952694X-RAY DIFFRACTION99
3.3307-3.53930.22221420.19462717X-RAY DIFFRACTION99
3.5393-3.81250.20481470.19372707X-RAY DIFFRACTION99
3.8125-4.1960.23031450.20562694X-RAY DIFFRACTION99
4.196-4.80270.19631430.18262724X-RAY DIFFRACTION99
4.8027-6.04910.20561510.20672753X-RAY DIFFRACTION99
6.0491-48.87540.2571490.23932844X-RAY DIFFRACTION96
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)
11.871-0.95521.21241.5203-0.84090.8283-0.0776-0.0059-0.17910.5478-0.02270.1363-0.244-0.03060.10390.4117-0.12460.12070.40320.01150.311-49.4241-22.5869-35.13
22.09820.42470.26731.47210.24840.17820.07930.0575-0.00230.3764-0.11140.1499-0.2967-0.26920.11910.3370.02410.02720.22110.00160.1613-42.1951-4.4699-38.6512
31.8007-0.5328-0.61941.5425-0.12481.29490.0397-0.26-0.06490.4062-0.12810.0156-0.309-0.15340.02470.3859-0.0896-0.04650.16180.04230.1734-31.1113-8.6569-28.4093
41.88350.4148-0.63322.1292-0.15511.74620.1321-0.2252-0.17030.5737-0.2899-0.11510.0649-0.0712-0.03980.4063-0.0501-0.07040.10110.0990.2045-30.1369-25.1415-33.5328
50.8869-0.0054-0.44111.92320.05310.32220.0372-0.1015-0.02920.2723-0.0642-0.1632-0.06030.24810.1410.2845-0.068-0.06460.18710.01620.185-19.934313.0478-34.7253
61.52730.42620.75281.79540.46260.3950.0887-0.12410.08370.4994-0.1626-0.1805-0.07780.07530.03270.3479-0.0425-0.06010.1345-0.03830.131-16.918330.7374-33.5954
72.5221-0.3526-1.20752.1416-0.04810.97690.0982-0.07130.07030.4037-0.1432-0.4429-0.08250.17870.06390.2214-0.1469-0.14230.26160.02270.2621-1.334329.3209-31.5512
82.48551.5190.11162.8971-0.15620.67510.0248-0.0061-0.11730.2733-0.1498-0.45130.03260.30490.11240.28670.0223-0.10450.26990.00920.3578-2.505913.9566-34.7518
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 39:125)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 126:236)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 237:354)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 355:490)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 38:117)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 118:249)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 250:358)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 359:490)

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