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- PDB-3e4b: Crystal structure of AlgK from Pseudomonas fluorescens WCS374r -

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Basic information

Entry
Database: PDB / ID: 3e4b
TitleCrystal structure of AlgK from Pseudomonas fluorescens WCS374r
ComponentsAlgK
KeywordsPROTEIN BINDING / AlgK / tetratricopeptide repeat / superhelix / alginate biosynthesis / Pseudomonas
Function / homologyTetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsKeiski, C.-L. / Harwich, M. / Jain, S. / Neculai, A.M. / Yip, P. / Robinson, H. / Whitney, J.C. / Burrows, L.L. / Ohman, D.E. / Howell, P.L.
Citation
Journal: Structure / Year: 2010
Title: AlgK is a TPR-containing protein and the periplasmic component of a novel exopolysaccharide secretin.
Authors: Keiski, C.L. / Harwich, M. / Jain, S. / Neculai, A.M. / Yip, P. / Robinson, H. / Whitney, J.C. / Riley, L. / Burrows, L.L. / Ohman, D.E. / Howell, P.L.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Expression, purification, crystallization and preliminary X-ray analysis of Pseudomonas fluorescens AlgK
Authors: Keiski, C.-L. / Yip, P. / Robinson, H. / Burrows, L.L. / Howell, P.L.
History
DepositionAug 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AlgK
B: AlgK
C: AlgK
D: AlgK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,94011
Polymers198,4654
Non-polymers4757
Water15,367853
1
A: AlgK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6522
Polymers49,6161
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AlgK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7443
Polymers49,6161
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: AlgK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8364
Polymers49,6161
Non-polymers2203
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: AlgK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7082
Polymers49,6161
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.090, 107.820, 119.030
Angle α, β, γ (deg.)90.00, 96.97, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
AlgK


Mass: 49616.281 Da / Num. of mol.: 4 / Mutation: C1M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: WCS374r / Gene: algK / Plasmid: pET26a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 CodonPlus (DE3)
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 853 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.54 Å3/Da / Density % sol: 51.54 %
Crystal growTemperature: 293 K / pH: 6
Details: 10% (w/v) PEG 6000, 0.1M MES pH 6.0, 0.56mM CYMAL-6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 4, 2006
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionRedundancy: 14.4 % / Number: 706639 / Rmerge(I) obs: 0.109 / Χ2: 2.29 / D res high: 2.8 Å / D res low: 30 Å / Num. obs: 49085 / % possible obs: 99.2
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancy
6.023099.60.076.54913.7
4.786.02110099.60.0913.97514.5
4.184.78396099.50.0873.12714.9
3.84.18363899.40.1062.39115.1
3.533.8821699.20.1511.81715.2
3.323.532296099.10.2051.46915.3
3.153.321470498.90.2891.06615.4
3.023.15652998.90.4430.85615.2
2.93.02755898.80.5980.73313.8
2.82.998.60.6940.68910.9
ReflectionResolution: 2.5→50 Å / Num. obs: 68665 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.49 % / Biso Wilson estimate: 50.46 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 14.96
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 7.53 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.8 Å / D res low: 30 Å / FOM : 0.34 / Reflection: 44926
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se600.6380.3920.0571.174
2Se600.2080.3240.4421.257
3Se600.3360.4010.6941.188
4Se600.2120.4830.3471.247
5Se600.4630.1620.1441.127
6Se600.810.5190.9690.967
7Se600.7480.4180.8240.895
8Se600.0520.5670.4740.872
9Se600.3990.2360.2740.871
10Se600.9770.4040.2380.785
11Se600.5840.3240.9850.92
12Se600.9390.3540.2260.781
13Se600.2050.590.0520.83
14Se600.960.6080.7521.039
15Se600.4160.1460.0960.727
16Se600.9590.280.8750.723
17Se600.20.730.5150.658
18Se600.440.4040.550.67
19Se600.3820.0970.7140.599
20Se600.9280.5570.7440.48
21Se54.870.380.2330.3230.442
22Se600.070.4690.5370.587
Phasing MAD shell
Resolution (Å)FOM Reflection
9.85-300.512350
6.29-9.850.513993
4.95-6.290.485071
4.2-4.950.455917
3.72-4.20.386596
3.37-3.720.297089
3.1-3.370.217120
2.89-3.10.136790
Phasing dmFOM : 0.61 / FOM acentric: 0.61 / FOM centric: 0.58 / Reflection: 44926 / Reflection acentric: 43432 / Reflection centric: 1494
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-29.4260.960.960.8820911888203
5-80.880.880.7164746139335
4-50.850.850.6980507763287
3.5-40.710.710.5579777739238
3-3.50.430.430.321326612965301
2.8-30.20.20.1570686938130

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLVE2.11phasing
RESOLVE2.11phasing
CNSrefinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 2.5→49.05 Å / Rfactor Rfree error: 0.005 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 3540 5.2 %RANDOM
Rwork0.22 ---
obs0.22 68663 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.59 Å2
Displacement parametersBiso mean: 48.79 Å2
Baniso -1Baniso -2Baniso -3
1--2.773 Å20 Å21.004 Å2
2--5.804 Å20 Å2
3----3.031 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→49.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11461 0 27 853 12341
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4691.5
X-RAY DIFFRACTIONc_mcangle_it2.3932
X-RAY DIFFRACTIONc_scbond_it2.4092
X-RAY DIFFRACTIONc_scangle_it3.5952.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 565 5 %
Rwork0.264 10815 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GOL_PARAM.TXTGOL_TOP.TXT
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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