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- PDB-8z78: Crystal structure of Procerain-B from Calotropis gigantea with gl... -

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Basic information

Entry
Database: PDB / ID: 8z78
TitleCrystal structure of Procerain-B from Calotropis gigantea with glycerol
ComponentsProcerain B
KeywordsHYDROLASE / plant protease / cystein peptidase / leaf latex
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: 1.9 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 with glycerol
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
Water3,333185
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)31.478, 91.697, 64.646
Angle α, β, γ (deg.)90.000, 90.000, 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 321 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_11PROPROSERSERAA129 - 321129 - 321
d_12GLYGLYTYRTYRAA325 - 339325 - 339
d_21PROPROTYRTYRBB129 - 339129 - 339

NCS oper: (Code: givenMatrix: (-0.999994941252, 0.00211615218754, -0.00237473601512), (-0.00209867309275, -0.999970867288, -0.00733894719016), (-0.00239019716177, -0.00733392626969, 0.999970249799) ...NCS oper: (Code: given
Matrix: (-0.999994941252, 0.00211615218754, -0.00237473601512), (-0.00209867309275, -0.999970867288, -0.00733894719016), (-0.00239019716177, -0.00733392626969, 0.999970249799)
Vector: -23.7012848278, -0.192901028721, -32.3533727191)

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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.: 185 / 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 pH 4.6, 65% PEG 400, 15% glycerol

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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: Oct 14, 2023 / 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: 0.45
ReflectionResolution: 1.9→45.85 Å / Num. obs: 28785 / % possible obs: 99.5 % / Redundancy: 5.3 % / Biso Wilson estimate: 13.53 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.067 / Rrim(I) all: 0.155 / Net I/σ(I): 12.1
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.625 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1799 / CC1/2: 0.765 / Rpim(I) all: 0.314 / Rrim(I) all: 0.702 / % possible all: 95.6

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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: 1.9→37.4 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.9044
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2131 1492 5.19 %
Rwork0.163 27267 -
obs0.1664 28759 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.57 Å2
Refinement stepCycle: LAST / Resolution: 1.9→37.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3315 0 0 185 3500
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473392
X-RAY DIFFRACTIONf_angle_d0.73074582
X-RAY DIFFRACTIONf_chiral_restr0.0526463
X-RAY DIFFRACTIONf_plane_restr0.007594
X-RAY DIFFRACTIONf_dihedral_angle_d16.02521242
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.8044389072 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.26841570.21522411X-RAY DIFFRACTION90.67
1.96-2.030.26331380.18462407X-RAY DIFFRACTION93.77
2.03-2.110.22181460.17842495X-RAY DIFFRACTION94.01
2.11-2.210.21531080.16342475X-RAY DIFFRACTION95.3
2.21-2.330.24351410.16612485X-RAY DIFFRACTION94.24
2.33-2.470.22761230.16292493X-RAY DIFFRACTION95.12
2.47-2.660.20261430.15642507X-RAY DIFFRACTION94.57
2.66-2.930.20791420.1542471X-RAY DIFFRACTION94.53
2.93-3.350.20861070.15932499X-RAY DIFFRACTION95.78
3.35-4.220.17551360.14452499X-RAY DIFFRACTION94.59
4.23-37.40.20321400.17342536X-RAY DIFFRACTION94.31
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)
11.01212247597-0.00385178086398-0.07512770576731.315349498220.1096460870031.17042026992-0.009019177526970.017299187808-0.0235191915954-0.0228358012715-0.00258251161873-0.08630755296290.03293969230330.1091670036560.002814202087130.06424568792990.001105080782280.02405184651280.1469460843210.02775720961220.0970414795292-4.21893108583-6.12031679895-3.14517871636
20.8380657617530.08046979928530.2460205936851.977709002970.2453070733231.50461660058-0.001334401548890.04794378390280.09690401018760.00929471253353-0.001432409636990.0122792887529-0.0933529865355-0.0125408768862-0.003706040283180.06871334370610.01307310177490.01285793991950.116693383040.03887357410340.079083944268-14.95005801573.4138003492-2.69075406703
31.843487753930.964105721142-0.1362391652755.832766218360.4391674601673.280057057350.0362188245430.3711629745630.0797303808627-0.142328078440.1218190277210.008421602051930.18172611136-0.153216634606-0.1058903177220.0635066744730.007539628568390.04150554916830.19390586570.03066100179140.109741395145-14.0966367186-2.24054525628-13.007539809
43.299938355063.21663815712-3.204746679944.22145482554-2.034271460594.38638083753-0.2032670523410.295037237636-0.675169395526-0.2344119676950.0841651183153-0.09024830128960.200412955756-0.2162182487860.1300128023680.142992879810.01111550523140.006314006335760.163900592121-0.003297182019540.160638030249-11.3844575841-22.27167186-7.37227074077
51.87992238526-0.00624483479186-0.8715984021191.62014016932-0.7467461700022.987071678460.1026545320440.0131769720014-0.06937266569260.1198795323550.1354099953540.01579970858280.0825967456533-0.0811212996671-0.1887027296860.114644535424-0.01675828515470.008409444171040.117719559297-0.01356980967570.049130580567-9.75563580545-14.82889856255.23566562502
63.4934574368-0.213976912533-1.03535299872.77255410983-0.4187256135762.9635883381-0.0270789012065-0.429090933289-0.08758629364560.2701082717450.08856902258190.089338873311-0.007205951784230.157472652628-0.02128472072240.17139766987-0.01545121654240.01591218468150.0954106730049-0.006160518841270.128190328247-8.21178672666-18.214842592212.2103384747
71.116614445360.265237034324-0.2544000937720.9053576940050.05538469312680.8247002190860.02444053979040.0559878037357-0.225564859820.0801093771935-0.00419532099195-0.04465573207690.1559009095860.00500045018396-0.03742148895910.0741541666797-0.00471961814040.01446206013290.109202700754-0.003769473351980.144017363066-5.63083858282-16.63865922011.97941133518
81.12340826089-0.01115026513920.22624115111.068113876830.20230993831.47024916032-0.02604206853440.143733337420.0345802872874-0.0227716268675-0.007807934241130.0836737550241-0.03762801417010.009001956429090.02865178049320.09370362364380.003948167889190.03722740756760.1577214932470.01330872205870.0874611153941-19.45213097416.03950573653-35.4909964464
92.51808515651-0.4452647022481.40316742472.26980821716-0.144130685621.54817314080.1922662579820.0286655002635-0.325099883801-0.0576302793748-0.127252590056-0.0854366979884-0.00964974253959-0.162654357625-0.0636201770220.09832796264210.02014499872080.02719774225110.181069982364-0.006797988555340.100863390673-8.46274184168-1.34838253393-34.3432297844
101.172778010170.2702493980520.09720937321811.99001448292-0.4499281610892.044405735920.020865718640.0665284149294-0.00574216087275-0.0122814609558-0.00806882120591-0.09314427852110.3452027989350.0433641298894-0.002493891493950.09638037343790.008822977501520.008480259230450.1967537780510.03664825006250.110190077689-8.92755011131-5.17079402623-35.4689644292
112.604991764431.5106597626-0.5153973067117.95813745354-0.6614460437663.44191088237-0.093072962552-0.0837681537152-0.0125172784207-0.321371392030.106695114039-0.255128049088-0.3243550246820.248914545928-0.003032670293660.1934433474-0.03121520137060.05958310982870.2491174961910.0112380022440.0967312932349-9.607912779092.06323945983-45.2722770406
121.515342699680.04572865640640.8580055477521.3647834220.4964846107082.76406571915-0.08587476823380.2271771728890.113198553851-0.05629461395630.0300882743063-0.026206325819-0.4236621584170.3456137510160.04743590261470.119871303423-0.01197981914070.01224656327660.1887087947060.02914912664420.135056563171-13.342613277517.9887181909-32.6261835321
131.24781785302-0.552239092474-0.08948125681071.665855598310.3945837751213.11248879799-0.0294893573372-0.330478901037-0.2220449156280.2205234602430.0006793362816720.0405184076923-0.002036187551344.71960294983E-50.02867955266690.190191325713-0.009375445985510.01902907127640.2582494687740.06424713671040.0787837780719-15.705005484717.6714233102-20.0365292407
141.06254694075-0.117847728402-0.03123368705461.309657122360.9209694840942.796052597240.0735136597945-0.1189877831060.179163097249-0.00344441846746-0.03854927344320.0421613093333-0.1811482062430.0923667346329-0.03336718158640.107168031793-0.009672727186290.02751368059290.140606473333-0.003514619711790.124538077828-18.443592457915.7575562319-30.3863634044
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 225 )AA170 - 22542 - 97
33chain 'A' and (resid 226 through 236 )AA226 - 23698 - 108
44chain 'A' and (resid 237 through 249 )AA237 - 249109 - 121
55chain 'A' and (resid 250 through 266 )AA250 - 266122 - 138
66chain 'A' and (resid 267 through 282 )AA267 - 282139 - 154
77chain 'A' and (resid 283 through 339 )AA283 - 339155 - 211
88chain 'B' and (resid 129 through 169 )BB129 - 1691 - 41
99chain 'B' and (resid 170 through 194 )BB170 - 19442 - 66
1010chain 'B' and (resid 195 through 225 )BB195 - 22567 - 97
1111chain 'B' and (resid 226 through 236 )BB226 - 23698 - 108
1212chain 'B' and (resid 237 through 266 )BB237 - 266109 - 138
1313chain 'B' and (resid 267 through 282 )BB267 - 282139 - 154
1414chain 'B' and (resid 283 through 339 )BB283 - 339155 - 208

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