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- PDB-5xq3: Crystal structure of a PL 26 exo-rhamnogalacturonan lyase from Pe... -

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Basic information

Entry
Database: PDB / ID: 5xq3
TitleCrystal structure of a PL 26 exo-rhamnogalacturonan lyase from Penicillium chrysogenum
Components(Pcrglx protein) x 2
KeywordsLYASE / exo-rhamnogalacturonan lyase / enzyme / pectin / SAD / Se
Function / homology
Function and homology information


lyase activity / metal ion binding
Similarity search - Function
YetA-like protein / : / : / : / PcRGLX-like N-terminal RIFT barrel domain / PcRGLX-like protein central beta sandwich domain / PcRGLX-like protein C-terminal alpha/alpha toroid domain
Similarity search - Domain/homology
Exo-rhamnogalacturonan lyase / Pc16g08050 protein
Similarity search - Component
Biological speciesPenicillium chrysogenum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsKunishige, Y. / Iwai, M. / Tada, T. / Nishimura, S. / Sakamoto, T.
CitationJournal: FEBS Lett. / Year: 2018
Title: Crystal structure of exo-rhamnogalacturonan lyase from Penicillium chrysogenum as a member of polysaccharide lyase family 26
Authors: Kunishige, Y. / Iwai, M. / Nakazawa, M. / Ueda, M. / Tada, T. / Nishimura, S. / Sakamoto, T.
History
DepositionJun 6, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2May 16, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 6, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pcrglx protein
B: Pcrglx protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,9674
Polymers201,8872
Non-polymers802
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9740 Å2
ΔGint-34 kcal/mol
Surface area57930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.471, 167.471, 172.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-1132-

HOH

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Components

#1: Protein Pcrglx protein


Mass: 101064.758 Da / Num. of mol.: 1 / Fragment: UNP residues 22-927
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium chrysogenum (fungus) / Gene: Pcrglx, EN45_041150 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A0A0C6EFY4, UniProt: B6H7Q7*PLUS
#2: Protein Pcrglx protein


Mass: 100822.484 Da / Num. of mol.: 1 / Fragment: UNP residues 22-927
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Penicillium chrysogenum (fungus) / Gene: Pcrglx, EN45_041150 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: A0A0C6EFY4, UniProt: B6H7Q7*PLUS
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3 Å3/Da / Density % sol: 58.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2.9 M Sodium Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→120.09 Å / Num. obs: 57725 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 33
Reflection shellResolution: 2.85→2.9 Å / Redundancy: 15 % / Mean I/σ(I) obs: 3 / Num. unique obs: 2860 / CC1/2: 0.886 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.85→120.09 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / SU B: 14.05 / SU ML: 0.263 / Cross valid method: THROUGHOUT / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23656 1956 3.5 %RANDOM
Rwork0.17103 ---
obs0.17329 54481 97.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.539 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.85→120.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13912 0 2 102 14016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01914340
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212754
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.93219595
X-RAY DIFFRACTIONr_angle_other_deg1.037329269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.47551781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.73923.835691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.257152032
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0951580
X-RAY DIFFRACTIONr_chiral_restr0.0930.22076
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02116655
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023521
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.1346.097127
X-RAY DIFFRACTIONr_mcbond_other4.1276.097126
X-RAY DIFFRACTIONr_mcangle_it6.139.1328898
X-RAY DIFFRACTIONr_mcangle_other6.139.1338899
X-RAY DIFFRACTIONr_scbond_it4.1376.2237213
X-RAY DIFFRACTIONr_scbond_other4.1366.2237213
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3079.25110695
X-RAY DIFFRACTIONr_long_range_B_refined8.32169.5216167
X-RAY DIFFRACTIONr_long_range_B_other8.32269.52516164
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.85→2.924 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 141 -
Rwork0.252 3855 -
obs--94.45 %

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