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- PDB-2b1n: Crystal structure of a papain-fold protein without the catalytic ... -

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Basic information

Entry
Database: PDB / ID: 2b1n
TitleCrystal structure of a papain-fold protein without the catalytic cysteine from seeds of Pachyrhizus erosus
Components
  • SPE31
  • peptide (LYS)(ALA)(SER)(VAL)(GLY)
KeywordsSUGAR BINDING PROTEIN / papain-like / peptide fragment
Function / homology
Function and homology information


cysteine-type peptidase activity / proteolysis
Similarity search - Function
Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily ...Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Papain-like protein SPE31
Similarity search - Component
Biological speciesPachyrhizus erosus (jicama)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsZhang, M. / Wei, Z. / Chang, S.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal structure of a papain-fold protein without the catalytic residue: a novel member in the cysteine proteinase family
Authors: Zhang, M. / Wei, Z. / Chang, S. / Teng, M. / Gong, W.
History
DepositionSep 16, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SPE31
B: peptide (LYS)(ALA)(SER)(VAL)(GLY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1563
Polymers27,5852
Non-polymers5711
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint8 kcal/mol
Surface area10020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.358, 61.358, 143.988
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein SPE31


Mass: 27123.848 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pachyrhizus erosus (jicama) / References: GenBank: 73623011, UniProt: Q3Y6U7*PLUS
#2: Protein/peptide peptide (LYS)(ALA)(SER)(VAL)(GLY)


Mass: 461.533 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: The peptide was chemically synthesized.
#3: Polysaccharide alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta- ...alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2-1/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.0M ammonium sulfate, 5% isopropyl alcohol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 25, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 11433 / % possible obs: 99.8 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.08 / Χ2: 1.049
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. measured obsΧ2Diffraction-ID
2.4-2.4699.58.70.5047541.0991
2.46-2.521008.90.4237221.121
2.52-2.5999.58.50.3887381.1371
2.59-2.661008.70.3447411.1461
2.66-2.7599.98.80.2727441.0991
2.75-2.8599.98.80.2297441.0821
2.85-2.9699.98.80.1757461.0391
2.96-3.091008.80.1337501.0521
3.09-3.2699.98.80.1067551.061
3.26-3.461009.20.0727580.9821
3.46-3.731009.20.0617640.9991
3.73-4.11009.20.0467751.0371
4.1-4.6999.990.0417761.0171
4.69-5.91008.90.0417970.9751
5.9-3098.58.10.0338690.9251

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT1.7data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→22.35 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 1340442.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 567 5 %RANDOM
Rwork0.206 ---
all0.209 ---
obs0.209 11366 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.308 Å2 / ksol: 0.364 e/Å3
Displacement parametersBiso mean: 33.6 Å2
Baniso -1Baniso -2Baniso -3
1--6.85 Å20 Å20 Å2
2---6.85 Å20 Å2
3---13.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.4→22.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1764 0 38 68 1870
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.62
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.329 86 4.6 %
Rwork0.258 1770 -
all-1856 -
obs--99.8 %

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