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- PDB-4lvo: Crystal structure of PfSUB1-prodomain-NIMP.M7 Fab complex with ad... -

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Basic information

Entry
Database: PDB / ID: 4lvo
TitleCrystal structure of PfSUB1-prodomain-NIMP.M7 Fab complex with added CaCl2
Components
  • (Subtilisin-like serine ...) x 2
  • NIMP.M7 Fab heavy chain
  • NIMP.M7 Fab light chain
KeywordsHYDROLASE/INHIBITOR/IMMUNE SYSTEM / alpha beta / enzyme-prodomain complex / Rossmann fold / serine protease / calcium ions / prodomain / parasitophorous vacuole / HYDROLASE-INHIBITOR-IMMUNE SYSTEM complex
Function / homology
Function and homology information


subtilisin / serine-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Alpha-Beta Plaits - #2380 / Peptidase S8A, subtilisin-like peptidase 1, plasmodium / SUB1 protease prodomain ProdP9 / SUB1 protease Prodomain ProdP9 / Subtilisin SUB1-like catalytic domain / : / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. ...Alpha-Beta Plaits - #2380 / Peptidase S8A, subtilisin-like peptidase 1, plasmodium / SUB1 protease prodomain ProdP9 / SUB1 protease Prodomain ProdP9 / Subtilisin SUB1-like catalytic domain / : / Peptidase S8/S53 domain / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Alpha-Beta Plaits / Immunoglobulins / Immunoglobulin-like / Sandwich / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Subtilisin-like protease 1 / Subtilisin-like protease 1
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsWithers-Martinez, C. / Blackman, M.J.
CitationJournal: Nat Commun / Year: 2014
Title: The malaria parasite egress protease SUB1 is a calcium-dependent redox switch subtilisin.
Authors: Withers-Martinez, C. / Strath, M. / Hackett, F. / Haire, L.F. / Howell, S.A. / Walker, P.A. / Evangelos, C. / Dodson, G.G. / Blackman, M.J.
History
DepositionJul 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Subtilisin-like serine protease
B: NIMP.M7 Fab light chain
C: NIMP.M7 Fab heavy chain
P: Subtilisin-like serine protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9597
Polymers95,8394
Non-polymers1203
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-58 kcal/mol
Surface area34360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.340, 76.030, 77.880
Angle α, β, γ (deg.)90.00, 102.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Subtilisin-like serine ... , 2 types, 2 molecules AP

#1: Protein Subtilisin-like serine protease


Mass: 38380.195 Da / Num. of mol.: 1 / Fragment: rPfSUB1cat (UNP residues 330-673)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: sub-1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q868D6, UniProt: O61142*PLUS, kexin
#4: Protein Subtilisin-like serine protease


Mass: 10509.888 Da / Num. of mol.: 1 / Fragment: rPfSUB1 Prodp9 (UNP residues 127-219)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: sub-1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q868D6, UniProt: O61142*PLUS, kexin

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Antibody , 2 types, 2 molecules BC

#2: Antibody NIMP.M7 Fab light chain


Mass: 23110.436 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody NIMP.M7 Fab heavy chain


Mass: 23838.588 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Non-polymers , 2 types, 204 molecules

#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

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Details

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

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.49 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3350, 0.2M ammonium formate, 150mM NaCl, 40mM CaCl2, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 30, 2013 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.26→76.17 Å / Num. all: 39382 / Num. obs: 38421 / % possible obs: 97.56 % / Observed criterion σ(F): 0.51 / Observed criterion σ(I): 5.88 / Redundancy: 3.4 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.08488 / Net I/σ(I): 11.69
Reflection shellResolution: 2.26→2.34 Å / Redundancy: 3 % / Rmerge(I) obs: 0.5007 / Mean I/σ(I) obs: 2.16 / Num. unique all: 3574 / % possible all: 91.69

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Processing

Software
NameVersionClassification
XDSdata scaling
PHENIXautoMRmodel building
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALEPACKdata scaling
PHENIXautoMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BH6 AND 1MLC

1bh6

1mlc


Resolution: 2.26→29.34 Å / SU ML: 0.24 / Isotropic thermal model: isotropic / σ(F): 1.34 / Phase error: 25.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2365 1922 5.01 %random
Rwork0.1913 ---
all0.1936 38421 --
obs0.1936 38398 97.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6441 0 3 201 6645
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046606
X-RAY DIFFRACTIONf_angle_d0.98987
X-RAY DIFFRACTIONf_dihedral_angle_d13.2382341
X-RAY DIFFRACTIONf_chiral_restr0.0621019
X-RAY DIFFRACTIONf_plane_restr0.0041155
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.31650.31061260.25212358X-RAY DIFFRACTION90
2.3165-2.37910.32741380.25082577X-RAY DIFFRACTION96
2.3791-2.44910.31181400.24172587X-RAY DIFFRACTION98
2.4491-2.52810.31691540.22752587X-RAY DIFFRACTION98
2.5281-2.61840.27881340.22652623X-RAY DIFFRACTION99
2.6184-2.72320.24771330.21952657X-RAY DIFFRACTION99
2.7232-2.8470.24181410.21562596X-RAY DIFFRACTION98
2.847-2.9970.2911240.21992564X-RAY DIFFRACTION96
2.997-3.18450.26631010.21372702X-RAY DIFFRACTION99
3.1845-3.430.25521300.20142656X-RAY DIFFRACTION100
3.43-3.77460.21651550.18162647X-RAY DIFFRACTION99
3.7746-4.31930.20441690.15312575X-RAY DIFFRACTION97
4.3193-5.43620.17971380.14492678X-RAY DIFFRACTION99
5.4362-29.3420.20541390.17572669X-RAY DIFFRACTION97
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)
12.7936-0.0763-0.01881.0345-0.0280.83580.0084-0.1514-0.00360.05020.0365-0.0205-0.0030.0162-0.03930.2357-0.02630.00820.212-0.01220.2979-45.8301-19.39932.3656
23.4635-0.1926-0.82271.1286-0.57461.77130.05030.30510.0905-0.01540.04950.2976-0.0554-0.2234-0.11820.278-0.0113-0.04210.2969-0.03250.4072-57.8142-16.6157-5.5251
32.45171.6252-0.44192.4949-0.53790.76310.0586-0.01550.3437-0.03080.09840.3991-0.1455-0.0977-0.12240.28820.02510.01540.2504-0.00260.4272-17.2965-3.6845-15.2771
41.49380.4834-0.57590.1769-0.61041.93210.01690.11840.0963-0.1251-0.04890.14550.06810.27040.04650.38990.0278-0.01420.36090.02610.3462-4.6263-11.3363-31.4538
52.3052-2.3796-2.60166.92836.37836.98040.35440.4712-0.0037-0.5664-0.21430.4793-0.0511-0.4651-0.09260.4024-0.0382-0.03790.4701-0.01660.3846-0.0419-8.1953-42.7602
64.6279-0.8726-3.06512.0427-0.4216.29560.14941.0797-0.5353-0.2112-0.30530.72830.1567-0.89640.18140.48490.01120.03460.7371-0.21840.7078-3.4101-15.9037-48.0155
72.1936-1.5749-1.85924.97823.93076.21120.08030.4685-0.0952-0.2105-0.2061-0.00090.1631-0.02430.16540.4952-0.0066-0.06140.64970.00470.34092.5932-10.6543-46.4363
81.9715-0.4266-0.91122.39610.45364.3215-0.07730.0153-0.2913-0.24730.1235-0.71090.16350.6288-0.10430.34160.00220.07020.42530.03950.6267-5.4932-29.3419-13.8785
91.52560.4637-1.20791.29950.10452.6776-0.0355-0.0041-0.0846-0.09340.0565-0.19450.10370.1310.01820.24190.0091-0.01510.23760.01120.3563-14.5174-25.0824-8.8689
104.0461-0.6493-2.27252.41431.4773.88730.05920.1826-0.51060.19190.17520.55350.5980.1936-0.37960.48040.01170.00650.3868-0.02720.4856-0.6203-31.3569-27.2452
113.8971-0.7159-1.42495.46332.57255.2467-0.07360.31780.1146-0.46130.1523-0.7589-0.33990.0142-0.02810.43040.01540.06840.57740.01890.340312.3357-15.957-39.7081
124.2314-0.22861.59363.1412.48432.899-0.11290.12240.2568-0.0298-0.15490.24160.25110.18180.28250.5034-0.0190.0130.52810.03350.31127.9803-16.5335-31.5018
137.1323-2.35732.774.13963.43176.70930.93140.87020.49950.7089-0.0703-0.6705-0.4641.4437-0.7040.5066-0.03270.03330.79970.00760.489320.1458-12.9692-34.8113
145.83351.88450.1178.7641-0.45714.30320.76580.7716-0.24670.36090.2620.00070.80750.0583-0.89010.6641-0.0058-0.0760.7043-0.02680.522916.451-23.4927-32.2264
152.76320.83770.09165.31060.81414.53480.0163-0.45690.604-0.1537-0.48270.0944-0.364-0.31580.42320.570.009-0.07050.9737-0.3490.7145-39.3026-0.811525.4139
163.48880.06751.7511.38021.05617.1998-0.2073-0.7320.14920.6619-0.0002-0.128-0.22220.23650.23420.5049-0.0209-0.00630.8267-0.22880.5328-34.5254-9.347225.8849
173.3636-0.7715-1.26552.60691.558.8286-0.1969-1.33510.09390.7197-0.28190.25320.7-0.82860.54020.8343-0.24690.16931.343-0.52630.6901-40.7503-11.413536.3475
181.11342.781.54019.63195.86435.75390.0387-0.86660.33690.4443-0.44990.67020.0527-0.78820.27870.4704-0.05110.07590.9121-0.1480.4876-48.3993-13.270622.0732
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 333 through 552 )
2X-RAY DIFFRACTION2chain 'A' and (resid 553 through 668 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 91 )
4X-RAY DIFFRACTION4chain 'B' and (resid 92 through 130 )
5X-RAY DIFFRACTION5chain 'B' and (resid 131 through 151 )
6X-RAY DIFFRACTION6chain 'B' and (resid 152 through 164 )
7X-RAY DIFFRACTION7chain 'B' and (resid 165 through 212 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1 through 17 )
9X-RAY DIFFRACTION9chain 'C' and (resid 18 through 113 )
10X-RAY DIFFRACTION10chain 'C' and (resid 114 through 126 )
11X-RAY DIFFRACTION11chain 'C' and (resid 127 through 152 )
12X-RAY DIFFRACTION12chain 'C' and (resid 153 through 191 )
13X-RAY DIFFRACTION13chain 'C' and (resid 192 through 206 )
14X-RAY DIFFRACTION14chain 'C' and (resid 207 through 219 )
15X-RAY DIFFRACTION15chain 'P' and (resid 139 through 159 )
16X-RAY DIFFRACTION16chain 'P' and (resid 160 through 185 )
17X-RAY DIFFRACTION17chain 'P' and (resid 186 through 203 )
18X-RAY DIFFRACTION18chain 'P' and (resid 204 through 217 )

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