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- PDB-8z6p: Crystal structure of Procerain-B from Calotropis gigantea -

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Basic information

Entry
Database: PDB / ID: 8z6p
TitleCrystal structure of Procerain-B from Calotropis gigantea
ComponentsProcerain B
KeywordsHYDROLASE / plant protease / cystein peptidase / leaf 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: 1.5 Å
AuthorsKumar, A. / Jamdar, S.N. / 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. / Makde, R.D.
History
DepositionApr 19, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 23, 2025Provider: 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 B
B: Procerain B


Theoretical massNumber of molelcules
Total (without water)77,4362
Polymers77,4362
Non-polymers00
Water5,386299
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)31.386, 91.361, 64.484
Angle α, β, γ (deg.)90.000, 89.984, 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 128 through 171 or resid 173...
d_2ens_1(chain "B" and (resid 128 through 171 or resid 173 through 209 or resid 211 through 339))

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_11LEULEUARGARGAA128 - 171128 - 171
d_12ILEILESERSERAA173 - 209173 - 209
d_13GLUGLUASNASNAA211 - 320211 - 320
d_14GLYGLYTYRTYRAA325 - 339325 - 339
d_21LEULEUARGARGBB128 - 171128 - 171
d_22ILEILESERSERBB173 - 209173 - 209
d_23GLUGLUTYRTYRBB211 - 339211 - 339

NCS oper: (Code: givenMatrix: (-0.999963878968, -0.00849843678543, -0.000131645346226), (0.00849705604471, -0.999929638605, 0.00827755265068), (-0.000201982341416, 0.00827613505906, 0.999965731809) ...NCS oper: (Code: given
Matrix: (-0.999963878968, -0.00849843678543, -0.000131645346226), (0.00849705604471, -0.999929638605, 0.00827755265068), (-0.000201982341416, 0.00827613505906, 0.999965731809)
Vector: -7.72115602171, 0.48374013182, 32.2848086954)

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Components

#1: Protein Procerain B


Mass: 38718.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calotropis (plant) / Organ: Leaf / Variant: Mumbai / Production host: Calotropis gigantea (mudar) / References: UniProt: A0A0A0Q2K8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 4.6 / Details: 0.2 M phospho-citrate buffer, pH 4.6, 65% PEG 400 / 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: Mar 15, 2024 / 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: 0.36
ReflectionResolution: 1.5→37.28 Å / Num. obs: 57532 / % possible obs: 99 % / Redundancy: 7.4 % / Biso Wilson estimate: 14.353 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.027 / Rrim(I) all: 0.075 / Net I/σ(I): 18.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.936 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2403 / CC1/2: 0.461 / Rpim(I) all: 0.427 / Rrim(I) all: 1.033 / % possible all: 84.4

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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: 1.5→30.4 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.7308
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1812 2844 4.95 %
Rwork0.1488 54659 -
obs0.1527 57503 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.06 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3323 0 0 299 3622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00523439
X-RAY DIFFRACTIONf_angle_d0.77684651
X-RAY DIFFRACTIONf_chiral_restr0.0778470
X-RAY DIFFRACTIONf_plane_restr0.007605
X-RAY DIFFRACTIONf_dihedral_angle_d14.86711269
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.587101514452 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.530.28931380.26012292X-RAY DIFFRACTION79.64
1.53-1.550.25941560.22792571X-RAY DIFFRACTION89.52
1.55-1.580.24851630.21012762X-RAY DIFFRACTION94.43
1.58-1.620.21951430.19882705X-RAY DIFFRACTION94.98
1.62-1.650.1861190.19212827X-RAY DIFFRACTION95.96
1.65-1.690.2071380.19412699X-RAY DIFFRACTION95.1
1.69-1.730.17641410.17492815X-RAY DIFFRACTION95.23
1.73-1.780.22081370.17352698X-RAY DIFFRACTION95.13
1.78-1.830.20091920.16552767X-RAY DIFFRACTION93.51
1.83-1.890.18251460.16422739X-RAY DIFFRACTION94.94
1.89-1.960.19391240.15732807X-RAY DIFFRACTION95.77
1.96-2.030.18541250.15572734X-RAY DIFFRACTION95.63
2.04-2.130.19631070.15122794X-RAY DIFFRACTION96.31
2.13-2.240.17381260.1512833X-RAY DIFFRACTION95.74
2.24-2.380.191470.14682730X-RAY DIFFRACTION94.89
2.38-2.560.17861200.14942781X-RAY DIFFRACTION95.86
2.56-2.820.16921540.14182765X-RAY DIFFRACTION94.72
2.82-3.230.19441510.14112777X-RAY DIFFRACTION94.84
3.23-4.070.15161500.12262759X-RAY DIFFRACTION94.84
4.07-30.40.16581440.1362827X-RAY DIFFRACTION95.12
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)
10.72318082841-0.118644827508-0.1285225295470.695463035239-0.06169368936460.808054736828-0.00789924559344-0.0592938543492-0.01260913156430.0330509609361-0.005009748779330.06023080761450.00839511025432-0.0346306318783-0.002203846163190.07431397758010.005973862870370.01014216705220.119322095155-0.005931250595380.157713972245-11.5274767104-6.42975182342-28.7689434939
27.077835216372.80215870686-3.288368841913.27738859424-1.694560849033.360161673660.10406296009-0.1388922781570.1102058572480.0502179472576-0.04242256287870.235203637105-0.00759028295812-0.181577704917-0.1182333952590.0726256164152-0.00305361907145-0.003631305758790.104359353263-0.02692526902020.15519727993-7.282976240473.31394962204-26.9765404908
31.42072830398-0.96634524318-1.609714951130.7120226042070.9763281278413.72759409789-0.0371693672249-0.09881014266320.06858052272630.01008381408250.0593710816945-0.017756802497-0.05392062848450.188758202152-0.04356543004650.0624138503716-0.005062456658990.005210465358220.138295934383-0.008846028991490.1811997390174.94303228334-1.85812752126-28.8847956433
40.7259352495720.7634694000260.00960226972541.17472532814-0.7075593255332.414759626090.0369930728915-0.06078227764420.1362828093760.0115810317682-0.0092532411410.049320578354-0.04711549779260.05131928577110.009768835001530.0602917484020.01782799997290.005370134147910.116066164832-0.02564647175090.161942689963-2.810653204765.23822599174-27.638176848
52.72163251408-0.669316211462-0.9141581155662.13364590960.1678233751622.67652684326-0.0253675772822-0.233535392518-0.3291927708960.1098142316820.0741828656345-0.2867102007390.1179897920390.2048189890270.01337038332740.127694954361-0.001628125953950.005121884320980.1486819138060.02020415508660.236006311245-4.23851643954-22.0268079104-24.8859969897
60.799740226038-0.0254669873604-0.05891025816081.120756524290.08052573323282.791806501910.0386773349050.0126076644971-0.0323025053611-0.0738255022030.0615825822531-0.02293501835770.1030891439240.0871065190673-0.01402161312430.07923334827890.007591306328140.01262659214560.117363070129-0.0002087192379020.146619491886-5.78528440413-14.7276013629-37.4749072294
71.200121092460.0670361087397-0.5108838044312.58997446451-0.2524388283012.87030491096-0.03198706904880.296659463906-0.0952609326511-0.1979577656850.0119062749548-0.09001746468510.0960684360754-0.0432627442364-0.01610846515170.1200556645650.009737633947650.01946956641750.140260670579-0.01508517042560.15695783241-7.53825359588-17.9478619903-44.3715411075
80.6768914194520.0400992881322-0.04637191615990.5761715410920.124553156541.13150757866-0.00763181615122-0.0157065946179-0.1310438762-0.01911121590950.02152855007180.05388449444130.0822777319149-0.00637793170634-0.01606166619590.0641895492027-0.002491758222620.01065785816320.1025469051690.00254236075480.174790125453-10.0542818149-16.4902033042-34.1993409246
90.359735185012-0.04690817500890.08618873146880.6012701773620.3522190251470.892051740066-0.0242621462939-0.03275851670750.0445576709773-0.02581572035490.0266362126312-0.0201395578869-0.08627742421990.0272117345354-0.0235043290840.108695990695-0.008378835129860.009319292216770.1973858637520.0162004472160.1613603720113.875511989756.621748387683.47762231058
103.17480073560.4934794319120.6000936783152.423895458050.2784125066091.46407769140.0652353363678-0.174743631541-0.06126026101730.086469559010.0540905836369-0.0201356946179-4.91821647139E-5-0.0259575251542-0.157105297210.0862785924264-0.008643367405970.01318064522050.145645097230.009780402240310.107182796955-6.40522796473-1.220429898652.29311740969
111.334262783080.0685912090939-0.09181394092221.814134621240.4733017748533.2498277946-0.0310509558473-0.0526129544001-0.01700082004840.04463459881250.06846871266650.07053911420340.16023765753-0.00495099490355-0.04673640321710.0589205913864-0.01304509236780.004920709377380.1488535742140.03113373017540.120496063348-6.39279743928-3.095540511445.63339665156
120.277444740104-0.2175351435660.4359436386310.799884837136-0.4393262547613.22231355536-0.00836397961925-0.0068380101610.108015620897-0.01412065751940.03702928641270.0177912050806-0.207301608311-0.0413052968839-0.0259156078380.0950383283785-0.008802490574970.01418123979630.1468204034470.004405866413770.1769380599030.8132425708316.796475791-2.82330004173
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 128 through 169 )AA128 - 1691 - 42
22chain 'A' and (resid 170 through 183 )AA170 - 18343 - 56
33chain 'A' and (resid 184 through 205 )AA184 - 20557 - 78
44chain 'A' and (resid 206 through 236 )AA206 - 23679 - 109
55chain 'A' and (resid 237 through 249 )AA237 - 249110 - 122
66chain 'A' and (resid 250 through 266 )AA250 - 266123 - 139
77chain 'A' and (resid 267 through 282 )AA267 - 282140 - 155
88chain 'A' and (resid 283 through 339 )AA283 - 339156 - 212
99chain 'B' and (resid 128 through 169 )BB128 - 1691 - 42
1010chain 'B' and (resid 170 through 194 )BB170 - 19443 - 67
1111chain 'B' and (resid 195 through 236 )BB195 - 23668 - 109
1212chain 'B' and (resid 237 through 339 )BB237 - 339110 - 208

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