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- PDB-2zzj: Crystal structure of endo-beta-1,4-glucuronan lyase from fungus T... -

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Basic information

Entry
Database: PDB / ID: 2zzj
TitleCrystal structure of endo-beta-1,4-glucuronan lyase from fungus Trichoderma reesei
ComponentsGlucuronan lyase A
KeywordsLYASE / beta-jelly roll
Function / homology
Function and homology information


lyase activity / metal ion binding
Similarity search - Function
Polysaccharide lyase / Polysaccharide lyase / Jelly Rolls - #200 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Glucuronan lyase A
Similarity search - Component
Biological speciesTrichoderma reesei (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsKonno, N. / Ishida, T. / Fushinobu, S. / Igarashi, K. / Habu, N. / Samejima, M. / Isogai, A.
Citation
Journal: Febs Lett. / Year: 2009
Title: Crystal structure of polysaccharide lyase family 20 endo-beta-1,4-glucuronan lyase from the filamentous fungus Trichoderma reesei.
Authors: Konno, N. / Ishida, T. / Igarashi, K. / Fushinobu, S. / Habu, N. / Samejima, M. / Isogai, A.
#1: Journal: Appl.Environ.Microbiol. / Year: 2009
Title: Cloning of the Trichoderma reesei cDNA encoding a glucuronan lyase belonging to a novel polysaccharide lyase family.
Authors: Konno, N. / Igarashi, K. / Habu, N. / Samejima, M. / Isogai, A.
History
DepositionFeb 16, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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: Glucuronan lyase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5693
Polymers27,3371
Non-polymers2322
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.287, 62.301, 129.121
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 Glucuronan lyase A


Mass: 27336.814 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Extracellular / Source: (gene. exp.) Trichoderma reesei (fungus) / Strain: NBRC 31329 / Gene: glA / Plasmid: pPICZalpha / Production host: Pichia pastoris (fungus) / Strain (production host): KM71H / References: UniProt: B6F143, glucuronan lyase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.67 Å3/Da / Density % sol: 53.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 20% PEG3350, 5.0mM CaCl2, 0.2M ammonium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.000, 0.97877, 0.97926, 0.96403
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 20, 2008
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.978771
30.979261
40.964031
ReflectionResolution: 1.8→50 Å / Num. obs: 27647 / % possible obs: 98.5 % / Biso Wilson estimate: 17.9 Å2 / Rsym value: 0.067 / Net I/σ(I): 30.8
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 4 / Rsym value: 0.363 / % possible all: 96.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→34.94 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.722 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22346 1386 5 %RANDOM
Rwork0.18361 ---
obs0.18563 26237 98.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.035 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1936 0 14 316 2266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212009
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4021.8892736
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.35237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.1323.761117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12115286
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5271514
X-RAY DIFFRACTIONr_chiral_restr0.1070.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021643
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.2877
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21340
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0480.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.221
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0111.51197
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.60221884
X-RAY DIFFRACTIONr_scbond_it2.2513957
X-RAY DIFFRACTIONr_scangle_it3.1844.5852
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.799→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 90 -
Rwork0.254 1853 -
obs--95.86 %

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