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- PDB-8jcr: Crystal structure of Procerain from Calotropis gigantea (pH 6.0) -

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Basic information

Entry
Database: PDB / ID: 8jcr
TitleCrystal structure of Procerain from Calotropis gigantea (pH 6.0)
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: 1.4 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)23,8414
Polymers23,3111
Non-polymers5313
Water3,513195
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)68.675, 120.980, 61.024
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: natural isolated from leaf latex / Source: (natural) Calotropis gigantea (mudar) / Plasmid details: Leaf latex / Variant: local / Strain: Mumbai / Tissue: Leaf
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 55.58 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 6
Details: 0.1 M MMT (L-Malic acid, MES, Tris) buffer pH 6.0, 25% PEG 1500
Temp details: constant 293

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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 20, 2021 / Details: Mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97893 Å / Relative weight: 1
ReflectionResolution: 1.4→42.96 Å / Num. obs: 50390 / % possible obs: 100 % / Redundancy: 11.2 % / Biso Wilson estimate: 15.74 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.018 / Rrim(I) all: 0.062 / Net I/σ(I): 22.5
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 10.3 % / Rmerge(I) obs: 1.19 / Mean I/σ(I) obs: 2 / Num. unique obs: 2472 / CC1/2: 0.764 / Rpim(I) all: 0.385 / Rrim(I) all: 1.251 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→34.77 Å / SU ML: 0.1516 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.9297
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1738 2468 4.9 %
Rwork0.1594 47889 -
obs0.16 50357 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.08 Å2
Refinement stepCycle: LAST / Resolution: 1.4→34.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1637 0 35 195 1867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841765
X-RAY DIFFRACTIONf_angle_d0.95572395
X-RAY DIFFRACTIONf_chiral_restr0.0855252
X-RAY DIFFRACTIONf_plane_restr0.0083313
X-RAY DIFFRACTIONf_dihedral_angle_d16.3328653
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.30611520.31172611X-RAY DIFFRACTION99.89
1.43-1.460.29151340.26742634X-RAY DIFFRACTION100
1.46-1.490.26011140.22452649X-RAY DIFFRACTION99.96
1.49-1.520.22421130.18572656X-RAY DIFFRACTION100
1.52-1.560.18121370.16472623X-RAY DIFFRACTION99.96
1.56-1.60.16151430.16112617X-RAY DIFFRACTION100
1.6-1.650.17311470.15542643X-RAY DIFFRACTION99.96
1.65-1.70.17941370.15722633X-RAY DIFFRACTION100
1.7-1.760.18721390.16882621X-RAY DIFFRACTION99.96
1.76-1.830.16431330.15462669X-RAY DIFFRACTION100
1.83-1.920.15931680.15252615X-RAY DIFFRACTION100
1.92-2.020.16111330.14062646X-RAY DIFFRACTION100
2.02-2.150.1561190.13882688X-RAY DIFFRACTION100
2.15-2.310.14751300.14832682X-RAY DIFFRACTION100
2.31-2.540.1661630.15052656X-RAY DIFFRACTION100
2.54-2.910.17491530.15552676X-RAY DIFFRACTION100
2.91-3.670.15611340.14972712X-RAY DIFFRACTION100
3.67-34.770.18441190.16342858X-RAY DIFFRACTION99.9
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)
15.590191638361.22834052343-0.486402238893.43893542917-1.379859026795.34595000349-0.1232988352920.21693248145-0.0271252760282-0.1554368580740.07031432809760.566766984859-0.137509796327-0.4728358215820.1243973302420.151475965390.00318671125583-0.03833523509260.147122851538-0.04788754708760.2455566259926.0310154230113.6592882179-4.52215822579
23.36517595286-0.116738866927-0.4676098643922.74465067171.068843492872.507164106560.037840667023-0.0687909998269-0.3220284963090.02251235366710.0443740483893-0.2754620635320.03846690693520.267984028481-0.08069876863510.108250524765-0.008033584928710.001089447058780.1059803241040.03152747074120.143385266327.636756964216.5187046503-0.11672611902
32.765969708070.66242534198-0.3587070723721.43459740672-0.2784225093461.222789345040.0451170941974-0.05613742555190.1062674327520.00137415177919-0.0161023212516-0.00722643474822-0.1434634326630.0872759188062-0.02390886519780.120259984261-0.0126749540015-0.0002095452950480.101689692655-0.00271912985540.10048192143925.185737035428.4441886759-0.876227660282
42.34828621961-0.3703779756350.2957747085052.40024505013-0.691911538741.859048080930.0502222164719-0.143769880857-0.1121383630360.2654020298650.0008853738447430.165379193397-0.0317206738351-0.0302899190532-0.0512490372420.134877230732-0.007873074120440.01642802128440.0952151307875-0.001890506338310.10683627139511.284835053216.95458784658.81855949648
51.589877618550.4112692957160.1671545675953.210736074141.133867047853.830173264340.0384232855094-0.256568805652-0.3028727698320.5190152955480.037505409168-0.1260217395560.2905111432640.171315658351-0.1193748923650.1868608699780.0199370307656-0.0315355677110.1721197800790.06343530703840.18194254037919.59248945486.6446789037813.217360737
62.370601869811.00390962902-0.04534341876332.328896980090.022045217260.922290000696-0.0273336618769-0.00564773475156-0.2245961177210.0266211994647-0.02255852710280.001141202155510.04869876653580.01750346761440.05376191003780.1069437876560.00725025626736-0.00114343181560.08347323018070.009358703681750.13246697139816.44267061359.07769379862.90081739849
72.28390247033-0.311669165611-1.104489956521.956735180520.9205622971522.20511398773-0.0630348273533-0.20045083527-0.2531569043570.237264365484-0.03416616932390.1688079727070.07833233019330.01085361211550.1480422472790.165569725045-0.002565301227590.009535857987990.1313681590230.03928286302190.18231301650310.15606699228.6261236918610.0571691422
82.523904977660.891842084113-0.9347329883313.66066884924-1.350462366473.064527276530.1068359253170.009007781774690.01688440956440.07956629221210.05767929834780.259229709448-0.0809622345429-0.0902043880135-0.1682925329780.116645404836-0.0001274696832490.008088569463520.131651271434-0.02025305808970.14947635017212.286983522322.4670584336.82426071748
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 135 )124 - 1351 - 12
22chain 'A' and (resid 136 through 149 )136 - 14913 - 26
33chain 'A' and (resid 150 through 234 )150 - 23427 - 111
44chain 'A' and (resid 235 through 263 )235 - 263112 - 140
55chain 'A' and (resid 264 through 279 )264 - 279141 - 156
66chain 'A' and (resid 280 through 310 )280 - 310157 - 187
77chain 'A' and (resid 311 through 323 )311 - 323188 - 200
88chain 'A' and (resid 324 through 337 )324 - 337201 - 214

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