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- PDB-1qcx: PECTIN LYASE B -

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Basic information

Entry
Database: PDB / ID: 1qcx
TitlePECTIN LYASE B
ComponentsPECTIN LYASE B
KeywordsLYASE / PECTIN LYASE / BETA-HELIX PROTEIN / PECTIN / PLANT CELL WALL
Function / homology
Function and homology information


pectin lyase / pectin lyase activity / pectate lyase activity / polysaccharide catabolic process / cell wall organization / extracellular region
Similarity search - Function
Pectate lyase / Pectin lyase family / Pectate lyase / Amb_all / 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
Biological speciesAspergillus niger (mold)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT, HEAVY ATOMS / Resolution: 1.7 Å
AuthorsVitali, J. / Jurnak, F.
CitationJournal: Plant Physiol. / Year: 1998
Title: The tree-dimensional structure of aspergillus niger pectin lyase B at 1.7-A resolution.
Authors: Vitali, J. / Schick, B. / Kester, H.C. / Visser, J. / Jurnak, F.
History
DepositionMay 13, 1999Processing site: BNL
Revision 1.0May 19, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PECTIN LYASE B


Theoretical massNumber of molelcules
Total (without water)37,8381
Polymers37,8381
Non-polymers00
Water6,107339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.700, 88.800, 42.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PECTIN LYASE B


Mass: 37837.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aspergillus niger (mold) / References: UniProt: Q00205, pectin lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.07 Å3/Da / Density % sol: 41 %
Crystal growpH: 5 / Details: pH 5.0
Crystal
*PLUS
Density % sol: 41 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMHEPES1drop
30.1 Mcitric acid1reservoir
41.6 Mammonium sulfate1reservoir
2protein1drop

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE(002) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 50124 / % possible obs: 73.8 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rsym value: 0.054 / Net I/σ(I): 18.9
Reflection
*PLUS
Num. measured all: 204035 / Rmerge(I) obs: 0.054

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Processing

Software
NameVersionClassification
SDMSSOFTWARE PACKAGEdata collection
SDMSSOFTWARE PACKAGEdata reduction
HEAVYmodel building
PHASESphasing
X-PLOR3.1model building
X-PLOR3.1refinement
SDMSdata scaling
HEAVYphasing
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, HEAVY ATOMS
Starting model: FOR MOLECULAR REPLACEMENT: PARALLEL BETA HELIX OF PELE, ALL AMINO ACIDS REPLACED WITH ALA UNLESS COMMON IN THE TWO PROTEINS; HEAVY ATOMS: PT, HG

Resolution: 1.7→7 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Cross valid method: R-FREE / σ(F): 2
Details: FREE R WAS USED UNTIL LAST CYCLE WHEN ALL DATA WAS INCLUDED
RfactorNum. reflection% reflectionSelection details
Rfree0.198 3204 10 %RANDOM
Rwork0.162 ---
obs0.162 32007 91.8 %-
Displacement parametersBiso mean: 17.5 Å2
Refinement stepCycle: LAST / Resolution: 1.7→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 0 339 3001
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.3
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2.9
X-RAY DIFFRACTIONx_scangle_it4.5
LS refinement shellResolution: 1.78→1.87 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.219 411 10.6 %
Rwork0.204 3462 -
obs--90.4 %
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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