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

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Basic information

Entry
Database: PDB / ID: 4azl
TitleIn meso structure of alginate transporter, AlgE, from Pseudomoas aeruginosa, PAO1, crystal form 2.
ComponentsALGINATE PRODUCTION PROTEIN ALGE
KeywordsMEMBRANE PROTEIN / OUTER MEMBRANE
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 / Alginate production protein AlgE
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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
DepositionJun 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 3, 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 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _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 1.6Feb 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

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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)106,56717
Polymers102,3992
Non-polymers4,16815
Water88349
1
A: ALGINATE PRODUCTION PROTEIN ALGE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1268
Polymers51,2001
Non-polymers1,9277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALGINATE PRODUCTION PROTEIN ALGE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4419
Polymers51,2001
Non-polymers2,2418
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.090, 245.760, 47.130
Angle α, β, γ (deg.)90.00, 104.36, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND RESSEQ 41:70 OR CHAIN A AND RESSEQ...
211CHAIN B AND RESSEQ 41:70 OR CHAIN B AND RESSEQ...

NCS oper: (Code: given
Matrix: (0.2006, -0.9767, 0.07659), (-0.01335, 0.07545, 0.9971), (-0.9796, -0.2011, 0.002101)
Vector: 28.04, 82.8, -34.78)

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Components

#1: Protein ALGINATE PRODUCTION PROTEIN ALGE / ALGE


Mass: 51199.520 Da / Num. of mol.: 2
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
#2: Chemical
ChemComp-78M / (2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE / 7.8 MONOACYLGLYCEROL


Mass: 314.460 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C18H34O4
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details(2RS)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE (78M/78N) ALKANE CHAINS WERE MODELLED AS 78M, BUT ...(2RS)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE (78M/78N) ALKANE CHAINS WERE MODELLED AS 78M, BUT COULD POSSIBLY BE OTHER DETERGENT.

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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: 2.59 Å3/Da / Density % sol: 52.51 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M SODIUM CACODYLATE, PH 6.5, 1.2 M SODIUM ACETATE

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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: Mar 5, 2010
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: 2.8→44.9 Å / Num. obs: 23738 / % possible obs: 93.2 % / Observed criterion σ(I): 2 / Redundancy: 2.7 % / Biso Wilson estimate: 36.86 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 5.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 2 / % possible all: 95.3

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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: 2.8→44.889 Å / SU ML: 0.47 / σ(F): 1.34 / Phase error: 29.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2803 1215 5.1 %
Rwork0.2371 --
obs0.2393 23738 93.35 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.245 Å2 / ksol: 0.296 e/Å3
Displacement parametersBiso mean: 44.24 Å2
Baniso -1Baniso -2Baniso -3
1--3.3652 Å20 Å2-0.6168 Å2
2--5.2082 Å20 Å2
3----1.8429 Å2
Refinement stepCycle: LAST / Resolution: 2.8→44.889 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6701 0 191 49 6941
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067048
X-RAY DIFFRACTIONf_angle_d1.2189488
X-RAY DIFFRACTIONf_dihedral_angle_d15.2792555
X-RAY DIFFRACTIONf_chiral_restr0.085952
X-RAY DIFFRACTIONf_plane_restr0.0051252
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2774X-RAY DIFFRACTIONPOSITIONAL
12B2774X-RAY DIFFRACTIONPOSITIONAL0.014
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.91210.36541210.32252556X-RAY DIFFRACTION95
2.9121-3.04460.39371510.30772551X-RAY DIFFRACTION95
3.0446-3.20510.3621350.28052521X-RAY DIFFRACTION95
3.2051-3.40580.27521250.23362558X-RAY DIFFRACTION95
3.4058-3.66870.2631220.21882504X-RAY DIFFRACTION94
3.6687-4.03770.27391520.21362488X-RAY DIFFRACTION94
4.0377-4.62140.21761250.18942509X-RAY DIFFRACTION93
4.6214-5.82050.22771480.20832454X-RAY DIFFRACTION92
5.8205-44.89510.29681360.27382382X-RAY DIFFRACTION89

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