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- PDB-4z4j: Crystal Structure of cellobiose 2-epimerase from Caldicellulosiru... -

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Basic information

Entry
Database: PDB / ID: 4z4j
TitleCrystal Structure of cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus DSM 8903
ComponentsCellobiose 2-epimerase
KeywordsISOMERASE / Cellobiose 2-epimerase / latulose / lactose
Function / homology
Function and homology information


cellobiose epimerase / cellobiose epimerase activity / carbohydrate metabolic process
Similarity search - Function
Cellobiose 2-epimerase / N-acylglucosamine 2-epimerase/Cellobiose 2-epimerase / N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
ISOPROPYL ALCOHOL / Cellobiose 2-epimerase
Similarity search - Component
Biological speciesCaldicellulosiruptor saccharolyticus DSM 8903 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.542 Å
AuthorsShen, Q.Y. / Zhang, Y.Z.
CitationJournal: to be published
Title: Crystal Structure of cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus DSM 8903
Authors: Shen, Q.Y. / Zhang, Y.Z.
History
DepositionApr 2, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cellobiose 2-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1337
Polymers47,7641
Non-polymers3686
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.687, 75.773, 91.171
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cellobiose 2-epimerase / CE


Mass: 47764.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor saccharolyticus DSM 8903 (bacteria)
Strain: DSM8903 / Gene: Csac_0294 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4XGA6, cellobiose epimerase
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.01 Å3/Da / Density % sol: 38.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Na citrate tribasic dihydrate pH 5.6, 20% v/v isopropanol, 20% v/v PEG 400

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.968 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 25, 2014
RadiationMonochromator: ID / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.54→30 Å / Num. obs: 55473 / % possible obs: 96.5 % / Redundancy: 13.8 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.029 / Rrim(I) all: 0.104 / Χ2: 0.996 / Net I/av σ(I): 21.709 / Net I/σ(I): 12 / Num. measured all: 766957
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Num. unique allCC1/2Rpim(I) allΧ2% possible allRmerge(I) obsRrim(I) all
1.54-1.5710.219960.7410.3921.00771.1
1.57-1.610.822220.7920.329178.1
1.6-1.6311.724360.8570.2750.99886.30.9170.959
1.63-1.6613.126990.9040.2371.00396.10.8530.887
1.66-1.6913.928500.9370.199199.70.7360.762
1.69-1.731428140.9580.1661.00799.60.6150.638
1.73-1.7813.928450.9720.1341.00699.80.4960.514
1.78-1.8314.128410.9760.1081.00199.80.4010.416
1.83-1.881428550.9820.0921.0011000.3410.354
1.88-1.9414.128510.9860.0720.99499.90.2670.277
1.94-2.0114.328470.9910.0570.9911000.2130.22
2.01-2.0914.428550.9940.0461.0211000.1710.177
2.09-2.1914.528600.9950.0380.9771000.1430.148
2.19-2.314.728590.9960.0331.0021000.1220.127
2.3-2.4414.728900.9970.0281.0251000.1040.108
2.44-2.6314.728820.9970.0240.9911000.0890.092
2.63-2.914.729060.9980.0210.9991000.080.083
2.9-3.3214.629150.9980.020.9631000.0750.077
3.32-4.1814.529570.9990.0160.9371000.0570.059
4.18-3013.530930.9980.0161.00899.40.0560.059

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MIR / Resolution: 1.542→29.625 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1877 2000 3.61 %thin shell
Rwork0.1587 ---
obs0.1597 55405 96.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.95 Å2 / Biso mean: 18.6559 Å2 / Biso min: 7.67 Å2
Refinement stepCycle: final / Resolution: 1.542→29.625 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3297 0 24 204 3525
Biso mean--25.87 26.95 -
Num. residues----392
Refinement TLS params.Method: refined / Origin x: 26.1514 Å / Origin y: 0.1351 Å / Origin z: -8.2895 Å
111213212223313233
T0.0942 Å2-0.0044 Å20.0021 Å2-0.0997 Å20.0019 Å2--0.0791 Å2
L0.8608 °20.0021 °2-0.0718 °2-1.1294 °2-0.1029 °2--0.9159 °2
S0.0012 Å °-0.0106 Å °-0.0648 Å °0.0146 Å °-0.0334 Å °-0.0091 Å °0.0342 Å °-0.0383 Å °0.0244 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-1 - 390
2X-RAY DIFFRACTION1allC2 - 125
3X-RAY DIFFRACTION1allC126 - 135
4X-RAY DIFFRACTION1allC136 - 142
5X-RAY DIFFRACTION1allC179 - 218
6X-RAY DIFFRACTION1allC219 - 230
7X-RAY DIFFRACTION1allC231
8X-RAY DIFFRACTION1allC232
9X-RAY DIFFRACTION1allC233 - 234
10X-RAY DIFFRACTION1allC236 - 237
11X-RAY DIFFRACTION1allC238 - 253
12X-RAY DIFFRACTION1allC254 - 284
13X-RAY DIFFRACTION1allC286
14X-RAY DIFFRACTION1allD1 - 2
15X-RAY DIFFRACTION1allE2 - 4
16X-RAY DIFFRACTION1allE5
17X-RAY DIFFRACTION1allE6

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