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- PDB-8jcs: Crystal structure of Procerain-B from Calotropis gigantea -

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Basic information

Entry
Database: PDB / ID: 8jcs
TitleCrystal structure of Procerain-B from Calotropis gigantea
ComponentsProcerain B
KeywordsHYDROLASE / plant protease / cystein peptidase / latex / Calotropis gigantea
Function / homology
Function and homology information


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 peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
Biological speciesCalotropis (plant)
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-B 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

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Assembly

Deposited unit
A: Procerain B
B: Procerain B


Theoretical massNumber of molelcules
Total (without water)77,4362
Polymers77,4362
Non-polymers00
Water3,873215
1
A: Procerain B


Theoretical massNumber of molelcules
Total (without water)38,7181
Polymers38,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Procerain B


Theoretical massNumber of molelcules
Total (without water)38,7181
Polymers38,7181
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.426, 91.466, 64.392
Angle α, β, γ (deg.)90.000, 90.019, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 129 through 320 or resid 325 through 339))
d_2ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11PROPROASNASNAA129 - 320129 - 320
d_12GLYGLYTYRTYRAA325 - 339325 - 339
d_21PROPROTYRTYRBB129 - 339129 - 339

NCS oper: (Code: givenMatrix: (-0.999986263352, 0.00502622830364, 0.00148665256924), (-0.00503964134534, -0.999945341778, -0.00916053885869), (0.00144052835177, -0.00916790521935, 0.999956936269) ...NCS oper: (Code: given
Matrix: (-0.999986263352, 0.00502622830364, 0.00148665256924), (-0.00503964134534, -0.999945341778, -0.00916053885869), (0.00144052835177, -0.00916790521935, 0.999956936269)
Vector: -23.8220969516, -0.186329777105, -32.2170411342)

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Components

#1: Protein Procerain B


Mass: 38718.238 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Calotropis (plant) / Plasmid details: Leaf latex / Variant: Mumbai / Tissue: Leaf / References: UniProt: A0A0A0Q2K8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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

Crystal growTemperature: 293 K / Method: batch mode / pH: 4.2 / Details: 0.2M phospho-citrate buffer pH 4.2, 55% PEG 200 / Temp details: constant

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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 2, 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
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 1.25→45.73 Å / Num. obs: 97592 / % possible obs: 97.3 % / Redundancy: 6.9 % / Biso Wilson estimate: 7.69 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.02 / Rrim(I) all: 0.055 / Net I/σ(I): 24.1
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 5.8 / Num. unique obs: 3705 / CC1/2: 0.916 / Rpim(I) all: 0.106 / Rrim(I) all: 0.227 / % possible all: 75.1

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→32.2 Å / Cross valid method: FREE R-VALUE / σ(F): 1.56 / Phase error: 19.6251
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.214 4761 4.88 %
Rwork0.1918 92794 -
obs0.2022 97555 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 8.71 Å2
Refinement stepCycle: LAST / Resolution: 1.25→32.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 0 215 3510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243371
X-RAY DIFFRACTIONf_angle_d0.53164552
X-RAY DIFFRACTIONf_chiral_restr0.0683460
X-RAY DIFFRACTIONf_plane_restr0.0053589
X-RAY DIFFRACTIONf_dihedral_angle_d13.89451234
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.576823900691 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.270.31871890.28733546X-RAY DIFFRACTION71.16
1.27-1.290.27522080.2824028X-RAY DIFFRACTION80.5
1.29-1.320.31062410.28184437X-RAY DIFFRACTION88.3
1.32-1.350.24562470.25234678X-RAY DIFFRACTION94.26
1.35-1.380.22322220.22754779X-RAY DIFFRACTION95.33
1.38-1.410.21562570.22254732X-RAY DIFFRACTION94.62
1.41-1.440.24182450.21154728X-RAY DIFFRACTION94.92
1.44-1.480.23122500.21154692X-RAY DIFFRACTION94.44
1.48-1.530.22082120.20474823X-RAY DIFFRACTION95.26
1.53-1.570.19862460.20274726X-RAY DIFFRACTION94.46
1.57-1.630.20472340.19684710X-RAY DIFFRACTION94.41
1.63-1.70.24862390.20254766X-RAY DIFFRACTION94.75
1.7-1.770.22492270.20574716X-RAY DIFFRACTION94.85
1.77-1.870.22532200.20824779X-RAY DIFFRACTION95.22
1.87-1.980.22982730.21624714X-RAY DIFFRACTION94.13
1.98-2.140.26842310.22264782X-RAY DIFFRACTION95.18
2.14-2.350.22472260.20854782X-RAY DIFFRACTION95.39
2.35-2.690.22982790.194763X-RAY DIFFRACTION94.37
2.69-3.390.18822370.17584801X-RAY DIFFRACTION95.16
3.39-32.20.19062290.15384861X-RAY DIFFRACTION95.37
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)
10.6028672320660.02540996642530.03503833616720.306519040963-0.1257930512110.263561558364-0.007292608097840.0296602757317-0.0391925049549-0.0259149335129-0.0136187034457-0.01940227129190.02873819298230.005670049099770.01732394428920.0165606417125-0.003261919840350.002482625328580.02552053488490.002809631584840.059387613829-4.33125287857-6.08098489461-3.20071104087
22.14748854558-0.403087701468-0.3550934361431.179249440280.1746720413220.8487397463190.03476079276580.1387215673240.0988221248212-0.0515610869903-0.00786604486012-0.0478524080133-0.01329376063710.0230251879036-0.02810071961550.0271770159212-0.00147497374324-0.002399823406170.02805261337680.008013894763010.0663964763746-9.227420566253.49540732318-4.88243600819
31.040089289740.286673639446-0.5176586514120.358097279879-0.2068700103181.33844574577-0.01273257181780.0575267724158-0.00796221251688-0.021156973610.02855105869140.0260876145635-0.0305711695453-0.0285607281728-0.01867398410540.01296905381580.000677045703909-0.004746492912450.03386069910590.003805292291110.0601580846412-20.7683105778-1.96893307038-3.25077237739
40.2596524796860.0184366492331-0.02744902131620.985209503642-0.1756475718131.532598785710.0162020928411-0.02716413892220.1370031334970.0008558141732450.02153873033610.021784204674-0.1523652855160.0331515012494-0.02485329903540.0448403396546-0.00915965373939-0.002363781532130.02096935444730.00164441558450.100798219908-12.79676012469.02531745648-0.3388930945
51.678225729840.369631813650.09979080952564.027383269070.5108012969151.26745590853-0.002241936101820.0682574973432-0.000256473476321-0.05700583315610.07454761437520.04199776684680.0613888761317-0.0874199757358-0.06313718562250.0282200225349-0.00344718637582-0.003119207735860.06209813735780.00656338866530.0290195687687-14.3569604996-2.27642210207-12.6782937797
60.427463851654-0.036580480015-0.07118254590810.6646483223110.01072951125720.8241291175070.00549703141613-0.0289141593521-0.09248712290760.03943471032470.01216955462190.01850551684740.0824892763513-0.0124450092266-0.008347170996680.0295690713979-0.002630238309750.002835852081970.02196322577590.006833902148340.0792925232318-6.87625889923-16.65522818333.87334998044
70.1150710779870.1946084741710.1243342030540.3475708784890.1488763308770.3269290471770.0347929583697-0.0300233580249-0.0822056580960.0292223945297-0.04206506732070.03103477387710.116691877103-0.0192996642986-0.005097488999250.050576433917-0.01182984169580.01649440396310.01509761479060.01106575225160.135513037692-5.77228135544-21.54304910113.44020251301
80.428646736031-0.1247418909590.1327473092690.56132132149-0.5982372084361.044920516210.06452222554610.067359295501-0.113361838725-0.00761841998763-0.07518427060590.0133349016977-0.02062089856840.00772507155994-0.01023479292040.00597201059383-0.03303392990130.0002686941206840.0268638272663-0.0007775610465320.0977557862884-12.769937164-15.0029353474-4.60236138441
90.419769912769-0.05813299266370.08182925875370.3379778037920.05268240784731.034452521620.02586568627890.01581451280010.00911824405605-0.0243074519568-0.01169451766960.0167191643386-0.0391211729532-0.0494420264941-0.01297064262310.06544935733470.002879013230480.004791075372630.11067394923-0.01094788089970.0373319736736-19.51374538996.00384312781-35.4065407228
100.765391979903-0.2427070218130.8021462598380.554564123971-0.3896169768691.194668097140.09567805576430.0314945891833-0.0664571128877-0.0886819558223-0.01967279148650.08399466733830.0303449235133-0.179711949782-0.06669049219220.1048478069290.0100614329175-0.0107942635250.183674916329-0.01947825719560.0427482373516-14.5333296451-3.5299482937-37.1228554491
110.2623991088080.156521310151-0.1105599124840.4825490173970.1080261293631.906714412470.02068733370390.0113085960831-0.002170399626730.0103537044698-0.0225910862564-0.0351281328270.07166048902670.048447388754-0.008761207168010.05730516394820.0099962119140.01597954170060.180016332655-0.02449375283860.0230182577217-3.117289952251.84612316843-35.5172463958
120.88169520498-0.0981764207439-0.5802981078182.114960419050.5492302497135.857723013540.00258268282329-0.0504101642511-0.1501062897130.0585989400318-0.0001504450347190.01411709205470.258061261469-0.006282871145910.008774224287710.07409872998840.002573009867330.009927666585990.115533211277-0.007869260634540.0601597120464-10.9664542408-9.07035951199-32.5486775076
131.500441444551.06665117304-0.5400271692064.24508338665-0.4694660877841.600163475420.0082494178154-0.05709296420050.00552881684852-0.2006779859230.0526078972324-0.114135082599-0.1425345488640.306207278248-0.04619350532050.0952790989321-0.02190723452630.0172447318470.179845631388-0.01391555208590.0402473208173-9.667477076752.09082103945-45.0827531914
140.899284301840.06278986612880.3958476639781.129596276050.3266145209761.820518878640.003078976879170.05675998579580.1093518023760.02975290015110.009642178962940.0235854994621-0.1126478730070.0304117489127-0.01196568976040.07521134859240.00560908944630.006775078956360.0991502738953-0.00128116876190.0477760243763-17.010399364816.4543942886-28.1963343287
151.87057025561-1.503881357350.004982268930082.45020814158-0.07567387134291.97459074578-0.06180200143390.1967911589740.48297681035-0.08988423006560.0864574944356-0.0108255420378-0.4335202599380.19801390525-0.03632292133120.198399691476-0.02087314089990.02043136048240.1137068271590.03568927010060.119617939543-19.694732486920.1772984049-28.7519375296
160.05237469598360.1802275352010.3858093094751.976638591952.260488716893.43938473074-0.034155877829-0.007274866129160.001896358878180.01148672779570.03625451707890.00499685822384-0.03874944182810.1482106799720.01240475982170.06235683827310.01020476247420.008239593965630.144902123311-0.01065058391520.0616896184742-11.199768573814.9099841317-36.6350948647
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 129 through 169 )AA129 - 1691 - 41
22chain 'A' and (resid 170 through 183 )AA170 - 18342 - 55
33chain 'A' and (resid 184 through 205 )AA184 - 20556 - 77
44chain 'A' and (resid 206 through 225 )AA206 - 22578 - 97
55chain 'A' and (resid 226 through 236 )AA226 - 23698 - 108
66chain 'A' and (resid 237 through 313 )AA237 - 313109 - 185
77chain 'A' and (resid 314 through 326 )AA314 - 326186 - 196
88chain 'A' and (resid 327 through 339 )AA327 - 339197 - 209
99chain 'B' and (resid 129 through 169 )BB129 - 1691 - 41
1010chain 'B' and (resid 170 through 183 )BB170 - 18342 - 55
1111chain 'B' and (resid 184 through 205 )BB184 - 20556 - 77
1212chain 'B' and (resid 206 through 225 )BB206 - 22578 - 97
1313chain 'B' and (resid 226 through 236 )BB226 - 23698 - 108
1414chain 'B' and (resid 237 through 313 )BB237 - 313109 - 185
1515chain 'B' and (resid 314 through 326 )BB314 - 326186 - 194
1616chain 'B' and (resid 327 through 339 )BB327 - 339195 - 207

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