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- PDB-2y2x: Crystal Structure of Pseudomonas Aeruginosa OpdK with Vanillate -

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Basic information

Entry
Database: PDB / ID: 2y2x
TitleCrystal Structure of Pseudomonas Aeruginosa OpdK with Vanillate
ComponentsVANILLATE PORIN OPDK
KeywordsMEMBRANE PROTEIN / OUTER MEMBRANE / OPRD / TRANSPORT
Function / homology
Function and homology information


porin activity / membrane
Similarity search - Function
Outer membrane porin, bacterial / outer membrane porin, OprD family / Porin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
4-HYDROXY-3-METHOXYBENZOATE / Vanillate porin OpdK
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA PA01 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsTouw, D.S. / Vijayaraghavan, J. / Vandenberg, B.
CitationJournal: To be Published
Title: Pseudomonas Aeruginosa Opdk with Vanillate
Authors: Touw, D.S. / Vijayaraghavan, J. / Vandenberg, B.
History
DepositionDec 16, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -9-STRANDED BARREL THIS IS REPRESENTED BY A -8-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: VANILLATE PORIN OPDK
B: VANILLATE PORIN OPDK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,79139
Polymers85,9872
Non-polymers9,80437
Water12,016667
1
A: VANILLATE PORIN OPDK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,68018
Polymers42,9941
Non-polymers4,68617
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: VANILLATE PORIN OPDK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,11121
Polymers42,9941
Non-polymers5,11720
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.142, 96.840, 121.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein VANILLATE PORIN OPDK / OPDK


Mass: 42993.523 Da / Num. of mol.: 2 / Fragment: RESIDUES 28-417
Source method: isolated from a genetically manipulated source
Details: AUTHORS INDICATE SIGNAL PEPTIDE REMOVED TO GIVE MATURE PROTEIN
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA PA01 (bacteria) / Plasmid: PB22 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9HUR5
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical...
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#4: Chemical
ChemComp-VNL / 4-HYDROXY-3-METHOXYBENZOATE / vanillate


Mass: 167.139 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H7O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE NUMBERING GIVEN IS FOR THE MATURE SEQUENCE.

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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: 2.88 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growDetails: 0.05 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, 26% PEG 400, PH 5.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→40 Å / Num. obs: 111761 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Biso Wilson estimate: 18.59 Å2 / Rmerge(I) obs: 0.06
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2 / % possible all: 89

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2QTK

2qtk


Resolution: 1.65→19.907 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 18.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 1945 1.7 %
Rwork0.1796 --
obs0.18 113038 96.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.605 Å2 / ksol: 0.411 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.1248 Å20 Å20 Å2
2--0.0029 Å20 Å2
3---2.1218 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5886 0 312 667 6865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066314
X-RAY DIFFRACTIONf_angle_d1.0598425
X-RAY DIFFRACTIONf_dihedral_angle_d15.9982337
X-RAY DIFFRACTIONf_chiral_restr0.083841
X-RAY DIFFRACTIONf_plane_restr0.0051089
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.69130.24521270.22857189X-RAY DIFFRACTION89
1.6913-1.7370.22341340.20277476X-RAY DIFFRACTION92
1.737-1.7880.24361340.19087641X-RAY DIFFRACTION94
1.788-1.84570.19771340.17417643X-RAY DIFFRACTION95
1.8457-1.91160.22241360.17177803X-RAY DIFFRACTION96
1.9116-1.98810.1941360.15797926X-RAY DIFFRACTION97
1.9881-2.07850.18321410.15288011X-RAY DIFFRACTION99
2.0785-2.18790.17161420.15748094X-RAY DIFFRACTION99
2.1879-2.32480.18441420.15938083X-RAY DIFFRACTION99
2.3248-2.5040.19571430.16918122X-RAY DIFFRACTION99
2.504-2.75540.21181410.17648191X-RAY DIFFRACTION99
2.7554-3.15280.19551440.18048235X-RAY DIFFRACTION100
3.1528-3.9670.17591450.17258323X-RAY DIFFRACTION100
3.967-19.90880.2271460.21058356X-RAY DIFFRACTION97
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)
11.241-0.4460.39720.41680.06670.4636-0.17150.33920.3610.1029-0.0257-0.2636-0.03040.19680.12540.142-0.02460.00450.24640.05940.1267-16.804321.4573-25.1409
20.33710.03120.25720.4215-0.0380.3495-0.07190.4209-0.17930.2316-0.05190.02310.09350.16530.05310.19810.03440.05520.3418-0.03580.1974-11.82946.7443-26.7279
30.8834-0.39680.35070.1266-0.00851.3577-0.06760.13410.0831-0.00760.0119-0.0281-0.2066-0.01660.05030.1498-0.01220.00870.10990.01420.1214-29.919918.568-13.492
41.01560.23720.11920.25240.00260.4389-0.030.0260.01760.04060.00530.05130.03320.0595-0.00870.0958-0.0048-0.00410.07520.01330.0853-13.986715.7846-3.5239
50.8195-0.18050.28060.0830.19950.4514-0.03410.31180.19170.0554-0.1083-0.10380.04420.1380.09490.12540.0224-0.00570.20040.01430.1312-15.0639-27.9726-24.5017
60.16940.00910.18670.18660.01870.30790.04220.3451-0.34850.0973-0.21080.0920.23330.13070.09040.25040.04180.03990.2834-0.05950.212-8.0824-44.0809-26.6848
71.1052-0.20560.13030.0920.10620.4102-0.02610.0633-0.01370.0135-0.04050.02130.0296-0.00480.05840.1186-0.00120.00870.0963-0.00320.1233-22.6423-30.7257-7.7653
80.5787-0.02230.0240.11350.19880.4407-0.00570.0481-0.04640.0104-0.01810.0312-0.01740.10630.01140.1320.0151-0.01130.12440.01940.1305-5.3885-33.6317-8.7531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 4:58)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 59:90)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 91:219)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 220:390)
5X-RAY DIFFRACTION5(CHAIN B AND RESID 4:61)
6X-RAY DIFFRACTION6(CHAIN B AND RESID 62:89)
7X-RAY DIFFRACTION7(CHAIN B AND RESID 90:321)
8X-RAY DIFFRACTION8(CHAIN B AND RESID 322:390)

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