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- PDB-8jcq: Crystal structure of Procerain from Calotropis gigantea -

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Basic information

Entry
Database: PDB / ID: 8jcq
TitleCrystal structure of Procerain from Calotropis gigantea
ComponentsProcerain
KeywordsHYDROLASE / plant protease / cystein peptidase / latex / Calotropis gigantea
Function / homologyBETA-MERCAPTOETHANOL / Chem-E64
Function and homology information
Biological speciesCalotropis gigantea (mudar)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsKumar, A. / Jamdar, S.N. / Srivastava, G. / Makde, R.D.
Funding support India, 1items
OrganizationGrant numberCountry
Other government India
CitationJournal: To Be Published
Title: Crystal structure of Procerain from Calotropis gigantea
Authors: Kumar, A. / Jamdar, S.N. / Srivastava, G. / Makde, R.D.
History
DepositionMay 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Procerain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7493
Polymers23,3111
Non-polymers4392
Water4,954275
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)68.616, 121.272, 61.006
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein Procerain


Mass: 23310.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: isolated from plant latex / Source: (natural) Calotropis gigantea (mudar) / Variant: Local / Strain: Mumbai / Tissue: leaf latex
#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30N5O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.77 Å3/Da / Density % sol: 55.64 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 9
Details: 0.1 M TBG (Tartrate, Bis-Tris, Glycylglycin) buffer pH 6.0 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97893 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2021 / Details: Mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.25→43.01 Å / Num. obs: 68894 / % possible obs: 98.1 % / Redundancy: 12.1 % / Biso Wilson estimate: 14.26 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.02 / Rrim(I) all: 0.072 / Net I/σ(I): 19.9
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2626 / CC1/2: 0.826 / Rpim(I) all: 0.257 / Rrim(I) all: 0.535 / % possible all: 76.8

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RESOLVEmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→43.01 Å / SU ML: 0.1024 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.8939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1824 3387 4.92 %
Rwork0.1639 65507 -
obs0.1648 68894 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.54 Å2
Refinement stepCycle: LAST / Resolution: 1.25→43.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 22 275 1934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01371764
X-RAY DIFFRACTIONf_angle_d1.29152396
X-RAY DIFFRACTIONf_chiral_restr0.1069251
X-RAY DIFFRACTIONf_plane_restr0.0115316
X-RAY DIFFRACTIONf_dihedral_angle_d15.0902661
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.23761000.2642091X-RAY DIFFRACTION74.96
1.27-1.290.25051230.22562423X-RAY DIFFRACTION87.94
1.29-1.310.21311270.21512549X-RAY DIFFRACTION93.8
1.31-1.330.1931420.2022683X-RAY DIFFRACTION97.68
1.33-1.350.22461530.19232740X-RAY DIFFRACTION99.62
1.35-1.380.19991520.18122757X-RAY DIFFRACTION100
1.38-1.40.19621440.18772743X-RAY DIFFRACTION99.97
1.4-1.430.21391520.18752765X-RAY DIFFRACTION99.97
1.43-1.460.2081400.19552738X-RAY DIFFRACTION100
1.46-1.50.19771150.18462794X-RAY DIFFRACTION99.97
1.5-1.540.20811280.16582779X-RAY DIFFRACTION99.97
1.54-1.580.18031410.16112769X-RAY DIFFRACTION100
1.58-1.620.18581730.15942745X-RAY DIFFRACTION100
1.62-1.680.18341230.15422785X-RAY DIFFRACTION100
1.68-1.740.1771710.16062745X-RAY DIFFRACTION100
1.74-1.810.19661190.16632800X-RAY DIFFRACTION100
1.81-1.890.17511700.16222759X-RAY DIFFRACTION100
1.89-1.990.16841530.15962781X-RAY DIFFRACTION100
1.99-2.110.17231290.14932805X-RAY DIFFRACTION100
2.11-2.270.17041420.15692809X-RAY DIFFRACTION100
2.27-2.50.1811620.16252792X-RAY DIFFRACTION100
2.5-2.870.18431570.16712817X-RAY DIFFRACTION100
2.87-3.610.16121460.16062838X-RAY DIFFRACTION100
3.61-43.010.18961250.15263000X-RAY DIFFRACTION99.87
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)
13.01069905360.918495123999-0.3040647751422.088652612340.2324652154291.58833185135-0.00804474704792-0.037971877497-0.377941213656-0.0721473685027-0.0297804045842-0.0996747644244-0.004790362009150.02472472918620.05222274066530.09825856196320.00282585192580.008934188242930.07076757585130.01618058448370.11424355211717.966658330118.1405273121-2.21278812735
25.043458922082.250085144190.5032980282641.993965039130.8336072074091.74876312947-0.1132827484230.143088035177-0.105226685585-0.2078125583380.107386471628-0.121673654826-0.234134991950.04586001857390.03172205320780.116746448829-0.004130934170520.0008573431853240.08502351106640.01196227940080.084223996663625.402747037826.6085208736-5.4400719409
32.584225840981.172253795340.5245505543810.954989652080.03554813297242.615922884820.40680908167-0.71245469560.3199820607420.284172170254-0.3324091904620.0276937205894-0.3037157995270.5211227756680.02487179099840.156160668299-0.0684492183432-0.0004363772445330.28051433723-0.02038685323820.079353081700225.192176731431.68291019756.44972667652
45.737964314410.3515825108030.9697029908073.76967043548-1.063574479612.23550703822-0.03435384135690.0123600964936-0.392069944607-0.0915229699538-0.043013571555-0.294951490409-0.005578482649050.2198957269630.05983653493670.106765340764-0.02195864400640.02117650405370.1324962721060.003935099370210.13758141699134.333936400128.1594601033-3.41536658085
57.745591900562.30433413328-4.837517561821.80799787284-2.175134915335.454353897720.0662480551360.08557381931140.3124346735110.01198874866610.1293921868040.127938799855-0.04299065965850.00130921009515-0.162726895730.1290605508880.0038142214079-0.02318739460280.0996404234388-0.007020652016650.097810400567418.263443671633.0939990748-3.39534633922
62.51591357151-0.4934405519260.6662058402191.19695016226-0.2490830502421.439747533230.0434860960007-0.36864449502-0.3223503217130.2540147137230.01420788311720.03903530401-0.0210904177615-0.0972375735163-0.06525672677570.135838313888-0.00715899860415-0.002238395533570.1257419147770.05032015215840.11837657952911.618744048517.17563913359.02446619814
71.292908677730.5235223330070.9707391822881.872407280811.028167394874.34000742250.0827561971329-0.492698307783-0.5228139147330.399647320897-0.0789128154051-0.1004475311950.1622665566670.144809739504-0.03529985951960.207153057694-0.00861487059549-0.05887033319360.2188189884920.1367286370250.32880650361320.04469236547.062012726713.175814831
81.322182448810.7572587133080.00190077223633.03114239720.2219300635580.548434736589-0.00730730191157-0.0689551677725-0.3445888137310.0211615670025-0.0604049629893-0.132526635460.06676452972470.02992127107180.07083675912280.1125964986470.005265540375990.004375408497340.08931850258480.03757651089170.19194316695516.44629716319.025243812932.77921421106
92.33460315182-0.493085247356-0.2382360921462.14736323440.7381149979661.56962219955-0.0774577338259-0.3631415101-0.4243616157160.282911552188-0.003042893810990.07958009271970.155567273174-0.05916949779820.07920679860570.1584968265-0.00577210791430.0008442374392740.1495538150940.08483057125790.20579538229810.62938006579.071813751989.91060862333
102.873506819650.783190595519-1.24754052385.83149410176-1.64899795141.492135349530.107085292507-0.009218359144640.0454278030531-0.09166832568520.1557278116250.2816758525280.0411266227929-0.148391239293-0.2713455523790.104105011318-0.00312887916554-0.003524727640950.122115133392-0.006871270131660.089905710489312.399188650224.18383125765.26628279909
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 124 through 165 )124 - 1651 - 42
22chain 'A' and (resid 166 through 181 )166 - 18143 - 58
33chain 'A' and (resid 182 through 203 )182 - 20359 - 80
44chain 'A' and (resid 204 through 223 )204 - 22381 - 100
55chain 'A' and (resid 224 through 234 )224 - 234101 - 111
66chain 'A' and (resid 235 through 263 )235 - 263112 - 140
77chain 'A' and (resid 264 through 279 )264 - 279141 - 156
88chain 'A' and (resid 280 through 310 )280 - 310157 - 187
99chain 'A' and (resid 311 through 323 )311 - 323188 - 200
1010chain 'A' and (resid 324 through 337 )324 - 337201 - 214

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