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- PDB-4qrg: Crystal structure of I86L mutant of papain -

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Basic information

Entry
Database: PDB / ID: 4qrg
TitleCrystal structure of I86L mutant of papain
ComponentsPapain
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: 2.497 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 1, 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: Papain
B: Papain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,2295
Polymers82,1352
Non-polymers943
Water2,036113
1
A: Papain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1614
Polymers41,0681
Non-polymers943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 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)42.722, 75.218, 116.463
Angle α, β, γ (deg.)90.000, 93.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Papain / / Papaya proteinase I / PPI


Mass: 41067.570 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-345 / Mutation: I86L, 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: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.27 Å3/Da / Density % sol: 45.93 % / Mosaicity: 0.364 °
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: 2.497→50 Å / Num. obs: 25630 / % possible obs: 99.8 % / Redundancy: 3.9 % / Biso Wilson estimate: 33.83 Å2 / Rmerge(I) obs: 0.11 / Χ2: 1.39 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.5-2.543.40.55612550.75997.4
2.54-2.593.60.53312520.6999.7
2.59-2.643.70.46912720.653100
2.64-2.693.80.44212910.623100
2.69-2.753.90.38812620.648100
2.75-2.823.90.31412750.66100
2.82-2.893.90.29312830.7100
2.89-2.963.90.26512560.755100
2.96-3.053.90.21112920.764100
3.05-3.153.90.16412670.774100
3.15-3.263.90.14513020.884100
3.26-3.393.90.11512540.858100
3.39-3.553.90.113051.044100
3.55-3.733.90.08612551.168100
3.73-3.973.90.07213121.194100
3.97-4.273.90.06412771.842100
4.27-4.73.90.0713022.089100
4.7-5.383.90.07612883.048100
5.38-6.783.90.06812893.04100
6.78-503.80.04113415.34999.6

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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: 2.497→39.339 Å / FOM work R set: 0.8497 / SU ML: 0.25 / σ(F): 1.34 / Phase error: 22.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 2011 7.85 %
Rwork0.1567 --
obs0.1619 25603 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 138.66 Å2 / Biso mean: 49.68 Å2 / Biso min: 12.18 Å2
Refinement stepCycle: LAST / Resolution: 2.497→39.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4799 0 3 113 4915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084923
X-RAY DIFFRACTIONf_angle_d1.0826658
X-RAY DIFFRACTIONf_chiral_restr0.043678
X-RAY DIFFRACTIONf_plane_restr0.005867
X-RAY DIFFRACTIONf_dihedral_angle_d14.1611784
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4972-2.55970.28751430.22391548169193
2.5597-2.62880.24051280.205816921820100
2.6288-2.70620.24861470.192417091856100
2.7062-2.79350.25491390.185716731812100
2.7935-2.89330.2711490.181216671816100
2.8933-3.00910.26031440.181816981842100
3.0091-3.1460.22361400.170116701810100
3.146-3.31180.26041440.161517111855100
3.3118-3.51920.24991380.163816891827100
3.5192-3.79070.21321500.141816861836100
3.7907-4.17180.18911400.13316981838100
4.1718-4.77460.17111480.124917211869100
4.7746-6.0120.21611460.146817011847100
6.012-39.34360.20461550.1471729188499
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)
12.4024-0.50070.53761.44660.14165.44420.03-0.494-0.20510.2666-0.07420.12840.6464-0.01310.00590.3526-0.01910.08210.23130.03670.29-7.4253-11.207278.2688
22.5912-0.6272-1.14322.66330.26942.46220.11380.13880.163-0.1962-0.18710.1329-0.55790.00180.150.2924-0.0380.00560.1441-0.00140.346-3.0580.427158.6602
32.37620.42650.06591.9115-0.11421.4338-0.01470.16420.0397-0.05220.0213-0.04980.04350.06040.01320.15440.02680.00310.10220.01410.20464.94012.602155.8646
46.80520.9595-0.82742.8016-0.22224.73720.1504-0.32050.5189-0.0492-0.01510.0229-0.34790.1292-0.15570.4071-0.0080.06640.3626-0.02710.235435.0866-3.2803-18.7483
53.16340.168-2.27713.1486-0.31875.4228-0.3014-0.3125-0.5162-0.0194-0.10520.12350.2064-0.00440.36360.39990.02610.02470.37150.01210.293625.3483-12.7147-9.0503
61.17110.7061-0.38674.6383-1.86863.58060.2432-0.3521-0.01110.848-0.19130.2395-0.49560.0318-0.0220.4354-0.10870.1080.43660.02150.382524.9593-16.84547.5038
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 4 THROUGH 74 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 75 THROUGH 113 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 114 THROUGH 319 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 3 THROUGH 58 )
5X-RAY DIFFRACTION5CHAIN B AND (RESID 59 THROUGH 106 )
6X-RAY DIFFRACTION6CHAIN B AND (RESID 107 THROUGH 319 )

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