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- PDB-4qrx: Crystal structure of pro-papain mutant at pH 4.0 -

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Basic information

Entry
Database: PDB / ID: 4qrx
TitleCrystal structure of pro-papain mutant at pH 4.0
Componentspro-papain
KeywordsHYDROLASE / protease / zymogen
Function / homology
Function and homology information


papain / serpin family protein binding / cysteine-type peptidase activity / proteolysis
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 speciesCarica papaya (papaya)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.138 Å
AuthorsDutta, S. / Choudhury, D. / Roy, S. / Biswas, S.
CitationJournal: to be published
Title: Pro-peptide regulates the substrate specificity and zymogen activation process of papain: A structural and mechanistic insight
Authors: Dutta, S. / Choudhury, D. / Roy, S. / Biswas, S.
History
DepositionJul 2, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: pro-papain
C: pro-papain


Theoretical massNumber of molelcules
Total (without water)82,1352
Polymers82,1352
Non-polymers00
Water1,31573
1
A: pro-papain


Theoretical massNumber of molelcules
Total (without water)41,0681
Polymers41,0681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: pro-papain


Theoretical massNumber of molelcules
Total (without water)41,0681
Polymers41,0681
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)42.592, 74.212, 116.233
Angle α, β, γ (deg.)90.000, 92.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein pro-papain / Papaya proteinase I / PPI


Mass: 41067.570 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-345 / Mutation: C132A, V139S, G143S, K281R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Carica papaya (papaya) / Plasmid: pET30 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00784, papain
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.23 Å3/Da / Density % sol: 44.95 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 7.5
Details: 8% PEG 4000, pH 7.5, hanging drop, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9737 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
ReflectionResolution: 3.138→50 Å / Num. obs: 12493 / % possible obs: 97.6 % / Redundancy: 3 % / Biso Wilson estimate: 56.83 Å2 / Rmerge(I) obs: 0.105 / Χ2: 0.947 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.15-3.22.80.4595520.77289.9
3.2-3.262.80.4135880.76391.4
3.26-3.332.90.3666000.85493.9
3.33-3.3930.3066030.81296.2
3.39-3.472.90.2746130.78897.8
3.47-3.552.90.2276620.81899.3
3.55-3.6430.1916120.81399.5
3.64-3.7330.1696330.82699.5
3.73-3.8430.1476350.81299.5
3.84-3.9730.1276310.93999.5
3.97-4.113.10.16390.98299.7
4.11-4.2730.0886420.92199.4
4.27-4.473.10.0776260.91199.4
4.47-4.730.0746450.96399.1
4.7-53.10.0736250.98699.2
5-5.3830.0736500.94399.2
5.38-5.9330.0886211.07298.4
5.93-6.7830.0846411.25998.2
6.78-8.5430.0546451.21797.4
8.54-502.90.0366301.39994.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.138→40.52 Å / FOM work R set: 0.7902 / SU ML: 0.4 / σ(F): 1.36 / Phase error: 28.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 610 4.89 %
Rwork0.1622 --
obs0.1669 12472 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 239.78 Å2 / Biso mean: 62.26 Å2 / Biso min: 8.64 Å2
Refinement stepCycle: LAST / Resolution: 3.138→40.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4782 0 0 73 4855
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014905
X-RAY DIFFRACTIONf_angle_d1.4296634
X-RAY DIFFRACTIONf_chiral_restr0.051677
X-RAY DIFFRACTIONf_plane_restr0.007864
X-RAY DIFFRACTIONf_dihedral_angle_d17.4041780
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1383-3.4540.31941510.20412783293493
3.454-3.95340.29081520.16613020317299
3.9534-4.97940.21241540.13813026318099
4.9794-40.52330.24391530.16433033318697
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.78650.9234-1.09491.93160.60825.67340.2313-0.27410.17020.1716-0.1360.30760.10650.26160.02540.35260.04920.07380.2593-0.01240.4548-4.6407-5.968571.155
24.39361.5121-0.17753.73070.42311.8813-0.00980.33680.1098-0.12890.0263-0.0679-0.01120.1246-0.00040.27940.06610.04170.24840.02710.27455.6433.052955.8891
32.6595-0.1532-1.96083.3895-0.86055.819-0.2566-0.04960.0032-0.20080.08950.06270.66420.14210.27160.4829-0.0250.10220.372-0.03910.352227.2549-10.4414-8.9799
43.2793-0.75930.78863.7551-1.24434.40890.0207-0.2979-0.22740.1718-0.0639-0.10010.01290.184-0.01370.3419-0.02910.0590.3433-0.01180.351625.6988-17.59297.156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 16 THROUGH 114 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 115 THROUGH 319 )
3X-RAY DIFFRACTION3CHAIN C AND (RESID 13 THROUGH 114 )
4X-RAY DIFFRACTION4CHAIN C AND (RESID 115 THROUGH 319 )

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