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- PDB-4lvn: Crystal structure of PfSUB1-prodomain-NIMP.M7 Fab complex -

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Basic information

Entry
Database: PDB / ID: 4lvn
TitleCrystal structure of PfSUB1-prodomain-NIMP.M7 Fab complex
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. / Peptidase S8, subtilisin, Asp-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 / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / 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
NICKEL (II) ION / 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: 2.25 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_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

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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)96,0779
Polymers95,8394
Non-polymers2385
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-69 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.500, 74.790, 78.850
Angle α, β, γ (deg.)90.00, 103.33, 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 , 3 types, 219 molecules

#5: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#6: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O

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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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% PEG 3350, 0.2M ammonium formate, 150mM NaCl, 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: I02 / Wavelength: 0.9795 Å
DetectorType: Pilatus 6M / Detector: PIXEL / Date: Sep 15, 2012 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.25→71.52 Å / Num. all: 39652 / Num. obs: 38990 / % possible obs: 98.33 % / Observed criterion σ(F): 2.22 / Observed criterion σ(I): 168.45 / Redundancy: 3.4 % / Biso Wilson estimate: 39.1 Å2 / Rmerge(I) obs: 0.1077 / Net I/σ(I): 7.95
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.67 / Num. unique all: 3930 / % possible all: 99.59

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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: 2.25→29.882 Å / SU ML: 0.23 / Isotropic thermal model: isotropic / σ(F): 1.36 / Phase error: 24.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 1951 5.01 %random
Rwork0.1953 ---
all0.1975 38990 --
obs0.1975 38909 98.17 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→29.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6400 0 5 214 6619
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046557
X-RAY DIFFRACTIONf_angle_d0.9388921
X-RAY DIFFRACTIONf_dihedral_angle_d12.6342309
X-RAY DIFFRACTIONf_chiral_restr0.0621018
X-RAY DIFFRACTIONf_plane_restr0.0041143
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30630.26851240.23422682X-RAY DIFFRACTION99
2.3063-2.36860.2851590.2232638X-RAY DIFFRACTION100
2.3686-2.43830.27341350.222656X-RAY DIFFRACTION100
2.4383-2.5170.28551450.22752656X-RAY DIFFRACTION99
2.517-2.60690.2851460.23582655X-RAY DIFFRACTION99
2.6069-2.71120.33461110.27242560X-RAY DIFFRACTION94
2.7112-2.83450.28521450.22712657X-RAY DIFFRACTION100
2.8345-2.98380.28471450.21852670X-RAY DIFFRACTION100
2.9838-3.17050.25971480.21482664X-RAY DIFFRACTION100
3.1705-3.4150.261430.20792598X-RAY DIFFRACTION97
3.415-3.75810.24231420.18872577X-RAY DIFFRACTION95
3.7581-4.30050.23481310.17252575X-RAY DIFFRACTION96
4.3005-5.41290.16071560.15122653X-RAY DIFFRACTION98
5.4129-29.88420.19431210.17432717X-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)
13.1827-0.47040.33191.82930.35390.6946-0.1346-0.0939-0.12770.12030.17260.0342-0.0150.0866-0.04810.25660.0140.03240.30820.03880.242976.26917.5122.9323
23.8095-0.28620.01152.15980.00971.1563-0.04460.30860.2449-0.14940.0684-0.0788-0.0884-0.1126-0.0610.15760.0218-0.01880.237-0.00620.222281.564419.9362-3.9879
31.66670.2011-0.382.46490.6952.8146-0.05750.59690.1657-0.2053-0.0563-0.3211-0.00630.096-0.01870.2218-0.04930.02450.2993-0.0040.354992.943525.8727-8.467
43.9420.2309-1.22850.66080.64952.09450.08390.27510.3057-0.2598-0.0668-0.34040.03830.1152-0.05960.1585-0.00610.02850.26820.00820.373998.545426.0741-6.3654
52.4242-1.3572-0.01027.4398-2.03481.5021-0.4594-0.66650.05131.12110.2782-0.9992-0.24750.8019-0.20050.27710.14990.01110.4813-0.03880.6062103.518519.74661.9322
63.25340.1579-0.72011.70550.5312.2402-0.1506-0.54690.23710.15390.2217-0.2763-0.06630.3156-0.01830.22730.0649-0.08440.3054-0.05660.304591.408524.48587.8196
72.3345-1.60080.37473.9015-0.14052.2094-0.0574-0.0620.18820.19210.103-0.1554-0.1228-0.04560.00920.2077-0.0179-0.00030.18690.03340.224854.155435.84514.9536
81.91170.6738-0.2823-0.0973-0.23641.32540.1351-0.3694-0.05240.2242-0.1942-0.03150.0889-0.51460.17960.3807-0.05240.01420.56450.07440.28241.758627.785331.2272
90.61341.0184-0.25434.7281-1.70882.3710.3924-0.94-0.3422-0.0794-0.595-0.5090.24860.01590.11890.4645-0.1178-0.08461.07170.23550.407938.329529.656639.8784
100.3448-0.41630.43350.4372-0.36531.83180.8298-0.1911-0.3180.9831-0.73830.4263-0.150.59980.15410.858-0.4081-0.00241.41480.1883-0.016735.606828.136849.7735
110.57070.0831-0.56112.86351.24891.2953-0.36640.6986-0.23350.7884-0.02250.5323-0.0891-0.39340.27990.3544-0.12370.04130.59760.17870.607642.394810.539712.4641
122.17420.3348-1.73471.64540.39242.5987-0.02710.0612-0.45250.12370.07980.29270.2011-0.0414-0.02370.21010.0422-0.03190.23840.10360.32351.374412.80749.2543
131.57320.382-0.2886-0.1189-0.19390.86730.2399-0.0053-0.03870.54860.09160.2284-0.4198-0.2997-0.31840.49790.0710.07040.37110.13850.428945.405818.936212.0025
143.53890.3280.01586.8028-1.68144.20330.1043-0.6446-0.0428-0.1259-0.50550.253-0.02770.02990.35560.40340.0357-0.05270.7845-0.02820.2824.531622.574734.116
150.7127-0.0151-1.42492.28770.62253.1666-0.04811.58640.5537-0.64780.22480.56680.0893-0.5149-0.01040.4412-0.0804-0.01740.95680.41580.631774.710434.8384-24.9771
169.08844.0077-4.38512.061-2.26822.4951.0899-0.69121.1897-0.3469-0.95360.0938-2.71871.515-0.06091.76-0.38510.14671.016-0.0770.551774.614520.607-35.3197
171.5703-2.01091.33253.6629-1.59171.15980.09430.29770.1273-1.28380.2679-0.09290.452-0.4036-0.18290.8953-0.03210.14861.09160.25720.577880.411832.6627-35.6485
181.8871-3.04531.98268.3871-3.20972.0841-0.07571.05870.3965-0.4131-0.1728-1.15640.20120.05230.34730.4920.08910.08050.93120.16710.413385.878926.9587-21.5353
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 334 through 427 )
2X-RAY DIFFRACTION2chain 'A' and (resid 428 through 497 )
3X-RAY DIFFRACTION3chain 'A' and (resid 498 through 530 )
4X-RAY DIFFRACTION4chain 'A' and (resid 531 through 561 )
5X-RAY DIFFRACTION5chain 'A' and (resid 562 through 582 )
6X-RAY DIFFRACTION6chain 'A' and (resid 583 through 669 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 91 )
8X-RAY DIFFRACTION8chain 'B' and (resid 92 through 130 )
9X-RAY DIFFRACTION9chain 'B' and (resid 131 through 175 )
10X-RAY DIFFRACTION10chain 'B' and (resid 176 through 212 )
11X-RAY DIFFRACTION11chain 'C' and (resid 1 through 17 )
12X-RAY DIFFRACTION12chain 'C' and (resid 18 through 99 )
13X-RAY DIFFRACTION13chain 'C' and (resid 100 through 126 )
14X-RAY DIFFRACTION14chain 'C' and (resid 127 through 220 )
15X-RAY DIFFRACTION15chain 'P' and (resid 137 through 185 )
16X-RAY DIFFRACTION16chain 'P' and (resid 186 through 190 )
17X-RAY DIFFRACTION17chain 'P' and (resid 191 through 203 )
18X-RAY DIFFRACTION18chain 'P' and (resid 204 through 217 )

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