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- PDB-6u7d: Recombinant stem bromelain precursor -

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Basic information

Entry
Database: PDB / ID: 6u7d
TitleRecombinant stem bromelain precursor
ComponentsFBSB
KeywordsPLANT PROTEIN / Pineapple cysteine protease
Function / homology
Function and homology information


proteolysis involved in protein catabolic process / lysosome / cysteine-type endopeptidase activity / extracellular space
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, asparagine active site / Eukaryotic thiol (cysteine) proteases asparagine active site. / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesAnanas comosus (pineapple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsYongqing, T. / Pike, R.N. / Wijeyewickrema, L.C.
Funding support Australia, 1items
OrganizationGrant numberCountry
Australian SIEF-industrial fellowship fund Australia
CitationJournal: To be published
Title: Crystal Structure of a Recombinant Stem Bromelain Precursor
Authors: Yongqing, T. / Pike, R.N. / Wijeyewickrema, L.C.
History
DepositionSep 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FBSB


Theoretical massNumber of molelcules
Total (without water)36,8711
Polymers36,8711
Non-polymers00
Water34219
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis, Gel electrophoresis of the recombinant stem bromelain precursor protein displays a single band of around 38 kDa, which is in agreement with the predicted mass ...Evidence: native gel electrophoresis, Gel electrophoresis of the recombinant stem bromelain precursor protein displays a single band of around 38 kDa, which is in agreement with the predicted mass based on the single polypeptide chain of recombinant protein.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area13080 Å2
Unit cell
Length a, b, c (Å)64.310, 69.940, 74.250
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein FBSB


Mass: 36871.297 Da / Num. of mol.: 1 / Fragment: UNP Residues 25-356
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ananas comosus (pineapple) / Tissue: Stem / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O23799, UniProt: A0A199VSS3*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.26 Å3/Da / Density % sol: 45.68 % / Description: Clear thin plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: A reservoir solution comprised of 19% (w/v) PEG6000, 0.01 M Zinc chloride and 0.1 M MMT, pH4. Using an equal reservoir to protein (8 mg/ml) ratio, crystals were observed after 1 day and grew ...Details: A reservoir solution comprised of 19% (w/v) PEG6000, 0.01 M Zinc chloride and 0.1 M MMT, pH4. Using an equal reservoir to protein (8 mg/ml) ratio, crystals were observed after 1 day and grew to maximal size after 2 week.
PH range: 3.8-4.2

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953695 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: May 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953695 Å / Relative weight: 1
ReflectionResolution: 3→47.38 Å / Num. obs: 7132 / % possible obs: 100 % / Redundancy: 14.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.095 / Rrim(I) all: 0.265 / Net I/σ(I): 10.7
Reflection shellResolution: 3→3.18 Å / Redundancy: 14.5 % / Rmerge(I) obs: 0.844 / Num. unique obs: 1130 / CC1/2: 0.903 / Rpim(I) all: 0.228 / Rrim(I) all: 0.879 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6OKJ

6okj


Resolution: 3→47.38 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.778 / SU B: 23.855 / SU ML: 0.423 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.564 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3138 323 4.6 %RANDOM
Rwork0.1982 ---
obs0.2032 6766 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.83 Å2 / Biso mean: 25.22 Å2 / Biso min: 3.66 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.31 Å2-0 Å2
3----0.32 Å2
Refinement stepCycle: final / Resolution: 3→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 0 19 2354
Biso mean---16.2 -
Num. residues----302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132394
X-RAY DIFFRACTIONr_bond_other_d0.0010.0182100
X-RAY DIFFRACTIONr_angle_refined_deg1.621.6393246
X-RAY DIFFRACTIONr_angle_other_deg1.2441.5754879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7385300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.93123.388121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.80715377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0191510
X-RAY DIFFRACTIONr_chiral_restr0.0640.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022732
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02522
LS refinement shellResolution: 3→3.078 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 25 -
Rwork0.296 491 -
all-516 -
obs--99.81 %

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