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- PDB-4nk6: Crystal Structure of the periplasmic alginate epimerase AlgG -

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Basic information

Entry
Database: PDB / ID: 4nk6
TitleCrystal Structure of the periplasmic alginate epimerase AlgG
ComponentsPoly(beta-D-mannuronate) C5 epimerase
KeywordsISOMERASE / AlgG / Pseudomonas / parallel beta-helix / alginate / mannuronate / polysaccharide epimerase / lysine methylation
Function / homology
Function and homology information


mannuronan 5-epimerase / alginic acid biosynthetic process / isomerase activity / ubiquitin-dependent protein catabolic process / regulation of apoptotic process / periplasmic space
Similarity search - Function
Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat-2 / Carbohydrate-binding/sugar hydrolysis domain / Domain present in carbohydrate binding proteins and sugar hydrolses / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold ...Right handed beta helix domain / Right handed beta helix region / Parallel beta-helix repeat-2 / Carbohydrate-binding/sugar hydrolysis domain / Domain present in carbohydrate binding proteins and sugar hydrolses / Parallel beta-helix repeat / Parallel beta-helix repeats / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
Mannuronan C5-epimerase
Similarity search - Component
Biological speciesPseudomonas syringae pv. tomato (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.0974 Å
AuthorsHowell, P.L. / Wolfram, F. / Robinson, H.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Catalytic Mechanism and Mode of Action of the Periplasmic Alginate Epimerase AlgG.
Authors: Wolfram, F. / Kitova, E.N. / Robinson, H. / Walvoort, M.T. / Codee, J.D. / Klassen, J.S. / Howell, P.L.
History
DepositionNov 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly(beta-D-mannuronate) C5 epimerase


Theoretical massNumber of molelcules
Total (without water)55,4061
Polymers55,4061
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Poly(beta-D-mannuronate) C5 epimerase

A: Poly(beta-D-mannuronate) C5 epimerase


Theoretical massNumber of molelcules
Total (without water)110,8132
Polymers110,8132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area1610 Å2
ΔGint-10 kcal/mol
Surface area31810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.616, 126.616, 97.708
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-605-

HOH

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Components

#1: Protein Poly(beta-D-mannuronate) C5 epimerase


Mass: 55406.293 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria)
Strain: DC3000 / Gene: algG, PSPTO_1238 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RP
References: UniProt: Q887Q3, Isomerases; Racemases and epimerases; Acting on carbohydrates and derivatives
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 4.08 Å3/Da / Density % sol: 69.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.26 M (NH4)2SO4, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 22, 2011
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionRedundancy: 22.1 % / Number: 699311 / Rmerge(I) obs: 0.137 / Χ2: 1.17 / D res high: 2.5 Å / D res low: 50 Å / Num. obs: 31575 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.385010010.1022.43221
4.275.3810010.0851.49521.8
3.734.2710010.0881.21722.1
3.393.7310010.1131.16422.2
3.153.3910010.1541.02622.4
2.963.1510010.2170.97222.4
2.822.9610010.2870.92522.5
2.692.8210010.3710.88122.5
2.592.6910010.5340.8722.4
2.52.5910010.640.77622.3
ReflectionResolution: 2.097→50 Å / Num. obs: 53161 / Rmerge(I) obs: 0.088
Reflection shellResolution: 2.097→2.18 Å / Redundancy: 21.5 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 6.8

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Phasing

PhasingMethod: SAD
Phasing dmFOM : 0.69 / FOM acentric: 0.69 / FOM centric: 0.61 / Reflection: 31146 / Reflection acentric: 28646 / Reflection centric: 2500
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-500.890.930.7614591143316
4.5-7.10.890.910.742583764494
3.6-4.50.880.890.7552934826467
3.1-3.60.780.790.6352634900363
2.7-3.10.580.590.4892768705571
2.5-2.70.390.390.3255975308289

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVE2.15phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: SAD / Resolution: 2.0974→47.813 Å / Occupancy max: 1 / Occupancy min: 0.95 / FOM work R set: 0.8403 / SU ML: 0.2 / σ(F): 1.34 / Phase error: 22.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2146 2003 3.79 %
Rwork0.1882 --
obs0.1893 52894 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 114.39 Å2 / Biso mean: 41.4669 Å2 / Biso min: 23.6 Å2
Refinement stepCycle: LAST / Resolution: 2.0974→47.813 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3354 0 0 167 3521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073420
X-RAY DIFFRACTIONf_angle_d1.1384632
X-RAY DIFFRACTIONf_chiral_restr0.079507
X-RAY DIFFRACTIONf_plane_restr0.004589
X-RAY DIFFRACTIONf_dihedral_angle_d13.0191272
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0974-2.14990.27561400.22493507364797
2.1499-2.2080.25411430.22136133756100
2.208-2.2730.33311400.3013450359096
2.273-2.34630.23591420.205136513793100
2.3463-2.43020.21481420.185336153757100
2.4302-2.52750.25311430.192136223765100
2.5275-2.64250.26421440.196336443788100
2.6425-2.78180.24751400.192436113751100
2.7818-2.95610.22731440.203336713815100
2.9561-3.18430.19611420.201136513793100
3.1843-3.50470.22341450.199736593804100
3.5047-4.01160.20511440.169736713815100
4.0116-5.05330.16151390.14653698383799
5.0533-47.82580.20721550.195538283983100
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)
11.9359-0.1209-0.15540.70230.32410.7080.40060.6276-0.6464-0.6354-0.43080.6149-0.042-0.27420.06630.51710.115-0.24810.5447-0.22180.5705-17.371347.1679-14.01
22.21860.87771.19433.62711.08530.7557-0.1333-0.2592-0.43050.5717-0.40851.0338-0.0269-0.6335-0.0740.2620.0632-0.04140.5889-0.14860.5491-28.369563.243812.8695
32.18310.1462-0.0851.24640.30721.64620.09230.08440.0653-0.3704-0.21780.4281-0.1889-0.49830.11130.34070.1486-0.16060.4995-0.12870.4918-26.895169.8014-1.2116
42.0005-0.5082-0.3062.16560.22691.3120.1022-0.04370.0443-0.2602-0.14590.2464-0.1007-0.34050.0730.24750.0746-0.0910.3887-0.07820.3043-15.690465.36751.2085
52.4798-1.2828-0.25442.41940.54771.37770.02620.0646-0.3571-0.3011-0.21520.35450.1529-0.28260.10160.24850.0016-0.08640.3534-0.08830.3135-13.627653.64680.8933
62.6255-0.6491-0.23082.2095-0.12711.50620.10940.0159-0.0895-0.2489-0.16160.08170.0778-0.12680.06660.24230.0134-0.0370.254-0.03680.27-0.70849.7841-1.3458
74.6227-0.5644-1.15671.4355-0.9274.80540.09550.046-0.1592-0.1765-0.10920.05780.18310.00130.0380.21990.0322-0.01980.2169-0.01370.31658.206642.3515-1.1665
84.4205-0.3086-1.07552.64-0.70894.4252-0.0532-0.8641-0.12580.3823-0.00150.2882-0.0635-0.2658-0.01190.26660.0188-0.0540.47390.02370.40038.112541.219110.6343
92.5403-1.60862.10886.05360.08912.55670.1676-0.0211-0.26930.02690.03770.04440.10910.0255-0.20080.26820.04360.00310.3458-0.02520.44418.157837.2794-2.7242
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 69 through 96 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 97 through 119 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 120 through 188 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 189 through 258 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 259 through 315 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 316 through 388 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 389 through 428 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 429 through 463 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 464 through 492 )A0

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