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- PDB-3sys: Improved crystal structure of Pseudomonas aeruginosa OccK1 (OpdK) -

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Basic information

Entry
Database: PDB / ID: 3sys
TitleImproved crystal structure of Pseudomonas aeruginosa OccK1 (OpdK)
ComponentsVanillate porin OpdK
KeywordsMEMBRANE PROTEIN / beta-barrel / channel / bacterial outer membrane
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
Authorsvan den Berg, B. / Eren, E.
CitationJournal: Plos Biol. / Year: 2012
Title: Substrate Specificity within a Family of Outer Membrane Carboxylate Channels.
Authors: Eren, E. / Vijayaraghavan, J. / Liu, J. / Cheneke, B.R. / Touw, D.S. / Lepore, B.W. / Indic, M. / Movileanu, L. / van den Berg, B.
History
DepositionJul 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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

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Assembly

Deposited unit
A: Vanillate porin OpdK
B: Vanillate porin OpdK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,67739
Polymers87,8732
Non-polymers9,80437
Water12,016667
1
A: Vanillate porin OpdK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,62318
Polymers43,9361
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)49,05421
Polymers43,9361
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


Mass: 43936.496 Da / Num. of mol.: 2 / Fragment: unp residues 28-417
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: opdK, PA4898 / Production host: Escherichia coli (E. coli) / 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

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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: 2.75 Å3/Da / Density % sol: 55.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 25% PEG 400 0.1 M Na-citrate 50 mM NaCl 25 mM Na-vanillate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 116995 / Num. obs: 116761 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 44.8
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2QTK

2qtk


Resolution: 1.65→19.907 Å / SU ML: 0.44 / σ(F): 0 / Phase error: 19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2007 1945 1.72 %
Rwork0.1813 --
obs0.1816 113061 96.69 %
all-116895 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.6 Å2 / ksol: 0.41 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.1248 Å20 Å2-0 Å2
2--0.0029 Å20 Å2
3---2.1218 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.907 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5861 0 312 667 6840
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066291
X-RAY DIFFRACTIONf_angle_d1.0388397
X-RAY DIFFRACTIONf_dihedral_angle_d16.3912331
X-RAY DIFFRACTIONf_chiral_restr0.081837
X-RAY DIFFRACTIONf_plane_restr0.0051086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6496-1.69090.25731260.23747138X-RAY DIFFRACTION88
1.6909-1.73650.2271330.20937489X-RAY DIFFRACTION92
1.7365-1.78760.24081340.19587642X-RAY DIFFRACTION94
1.7876-1.84530.1981350.17917657X-RAY DIFFRACTION95
1.8453-1.91120.21851350.17347793X-RAY DIFFRACTION96
1.9112-1.98760.19551380.16187937X-RAY DIFFRACTION97
1.9876-2.0780.18361410.15628022X-RAY DIFFRACTION99
2.078-2.18740.17231410.15878094X-RAY DIFFRACTION99
2.1874-2.32430.18581420.16098092X-RAY DIFFRACTION99
2.3243-2.50340.20251440.178125X-RAY DIFFRACTION99
2.5034-2.75480.20991410.17688195X-RAY DIFFRACTION99
2.7548-3.1520.19591440.1818243X-RAY DIFFRACTION100
3.152-3.96610.17871450.17328327X-RAY DIFFRACTION100
3.9661-19.90880.22141460.21168362X-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)
13.1954-1.14780.47980.71130.21610.7014-0.08220.44930.42850.0159-0.0893-0.2493-0.02270.1920.17760.1754-0.04360.00390.27320.04420.1621-16.803821.4566-25.1402
23.9497-0.44460.42810.6637-0.15171.9779-0.03530.516-0.67280.1611-0.06510.04950.42580.22540.13680.2630.02040.05120.3502-0.05260.2618-11.8316.7438-26.7296
31.4597-0.4570.25010.4442-0.06562.1195-0.07430.15390.1397-0.0360.0275-0.0299-0.2773-0.02360.04970.1392-0.01330.00440.10060.01860.1199-29.919518.5681-13.4917
41.58620.39660.15590.60190.08880.7556-0.0390.05170.02190.00210.01350.00870.02430.09740.02250.13070.0043-0.0040.10990.01230.1129-13.986815.7838-3.5233
52.8191-0.83330.40860.58190.3690.7944-0.00420.36930.27360.0329-0.1293-0.13190.0210.12780.14750.1736-0.00010.00140.23290.00340.1644-15.0644-27.9726-24.5008
64.9601-0.18310.12423.2751-0.6653.98950.00270.512-0.9486-0.1228-0.22440.03660.76820.17760.1910.30850.03770.06110.2729-0.09320.264-8.7275-43.4197-27.6689
71.5534-0.22510.16770.25740.01490.8207-0.02610.0801-0.0237-0.0053-0.03590.03980.05-0.0360.07010.11820.00330.01240.0957-0.00030.1227-22.6421-30.7253-7.7651
81.04140.1062-0.22450.9474-0.3611.5705-0.02510.0829-0.031-0.06180.01420.02910.01260.07470.00680.14050.0171-0.01780.15290.00760.1514-5.3884-33.6314-8.7532
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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