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- PDB-2nnr: Crystal structure of chagasin, cysteine protease inhibitor from T... -

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Basic information

Entry
Database: PDB / ID: 2nnr
TitleCrystal structure of chagasin, cysteine protease inhibitor from Trypanosoma cruzi
ComponentsChagasin
KeywordsHYDROLASE INHIBITOR / chagasin / deformed jelly roll / predominately beta structure
Function / homology
Function and homology information


ciliary pocket / cysteine-type endopeptidase inhibitor activity / cytoplasmic vesicle / cell surface
Similarity search - Function
Immunoglobulin-like - #2020 / Proteinase inhibitor I42, chagasin / Chagasin-like superfamily / Chagasin family peptidase inhibitor I42 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsRedzynia, I. / Bujacz, G. / Ljunggren, A. / Jaskolski, M. / Abrahamson, M.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of the parasite protease inhibitor chagasin in complex with a host target cysteine protease
Authors: Ljunggren, A. / Redzynia, I. / Alvarez-Fernandez, M. / Abrahamson, M. / Mort, J.S. / Krupa, J.C. / Jaskolski, M. / Bujacz, G.
History
DepositionOct 24, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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: Chagasin
B: Chagasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,88511
Polymers24,1092
Non-polymers7769
Water3,513195
1
A: Chagasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7038
Polymers12,0541
Non-polymers6497
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chagasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,1823
Polymers12,0541
Non-polymers1282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.546, 49.546, 187.576
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
Components on special symmetry positions
IDModelComponents
11A-3040-

HOH

21B-3048-

HOH

31B-3073-

HOH

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Components

#1: Protein Chagasin / cysteine protease inhibitor


Mass: 12054.476 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Plasmid: pGEX-6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q966X9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.36 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.5M Lithium Sulfate, 0.1M Hepes pH 8.5, protein concentration 8 mg/ml, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG X1110.8123
SYNCHROTRONEMBL/DESY, HAMBURG BW7A20.9792, 0.9797, 0.9763
Detector
TypeIDDetectorDate
MAR CCD 165 mm1CCDJan 25, 2005
MAR CCD 165 mm2CCDOct 18, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI (111)SINGLE WAVELENGTHMx-ray1
2SI (111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.81231
20.97921
30.97971
40.97631
Reflection

Av σ(I) over netI: 8.9 / Number: 61951 / Rmerge(I) obs: 0.098 / Χ2: 1.24 / D res high: 2.8 Å / D res low: 40 Å / Num. obs: 6796 / % possible obs: 100 / Redundancy: 9.1 %

ID
1
2
3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.034099.710.0551.7829.2
4.796.0310010.0741.6499.4
4.184.7910010.0721.5039.4
3.84.1810010.0881.3259.2
3.533.810010.1091.1839.4
3.323.5310010.1391.1079.3
3.153.3210010.2130.9789.4
3.023.1510010.3160.8939.2
2.93.0210010.4450.859.2
2.82.999.910.6071.0337.4
6.034099.720.0551.7829.2
4.796.0310020.0741.6499.4
4.184.7910020.0721.5039.4
3.84.1810020.0881.3259.2
3.533.810020.1091.1839.4
3.323.5310020.1391.1079.3
3.153.3210020.2130.9789.4
3.023.1510020.3160.8939.2
2.93.0210020.4450.859.2
2.82.999.920.6071.0337.4
6.034099.730.0551.7829.2
4.796.0310030.0741.6499.4
4.184.7910030.0721.5039.4
3.84.1810030.0881.3259.2
3.533.810030.1091.1839.4
3.323.5310030.1391.1079.3
3.153.3210030.2130.9789.4
3.023.1510030.3160.8939.2
2.93.0210030.4450.859.2
2.82.999.930.6071.0337.4
ReflectionResolution: 1.7→62.5 Å / Num. all: 29552 / Num. obs: 29434 / % possible obs: 99.6 % / Redundancy: 7.8 % / Biso Wilson estimate: 31.888 Å2 / Rmerge(I) obs: 0.038 / Χ2: 0.925 / Net I/σ(I): 38.3
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 4 / Num. unique all: 1435 / Χ2: 0.645 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
Auto-Rickshawphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→45 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1218 4.1 %RANDOM
Rwork0.186 ---
all0.188 29559 --
obs0.187 29404 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 42.594 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.46 Å20 Å2
2--0.91 Å20 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 1.7→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1702 0 48 195 1945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211862
X-RAY DIFFRACTIONr_angle_refined_deg1.5381.9472530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4695221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.12724.32181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30215290
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.273155
X-RAY DIFFRACTIONr_chiral_restr0.1190.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021393
X-RAY DIFFRACTIONr_nbd_refined0.2150.2741
X-RAY DIFFRACTIONr_nbtor_refined0.310.21209
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.220.2201
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1910.225
X-RAY DIFFRACTIONr_mcbond_it0.9991.51137
X-RAY DIFFRACTIONr_mcangle_it1.52521828
X-RAY DIFFRACTIONr_scbond_it2.3643813
X-RAY DIFFRACTIONr_scangle_it3.5434.5702
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 98 -
Rwork0.204 1958 -
obs-2056 97.35 %
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)
11.5419-0.80510.14416.51860.36390.3206-0.0636-0.0521-0.52220.32410.01980.8960.0978-0.18260.0438-0.03440.09840.0992-0.08680.04610.10796.36823.027312.4966
21.5862-0.0033-0.57694.442-1.05482.0003-0.05020.0122-0.4110.0360.02990.21840.19710.0280.0203-0.0660.12590.0309-0.11210.0293-0.030416.787319.971710.0159
30.4897-1.0034-1.32056.33794.21794.09480.2009-0.13760.26130.28860.113-0.4938-0.03710.3868-0.3139-0.02170.04360.014-0.0185-0.0735-0.059941.07298.874521.4188
40.91581.92251.63164.09743.04475.25850.1943-0.18010.3084-0.1733-0.41360.4143-0.4992-0.23320.2193-0.02010.09030.0553-0.0657-0.0778-0.036531.242413.119818.7907
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA2 - 72 - 7
21AA19 - 3219 - 32
31AA50 - 8050 - 80
42AA8 - 188 - 18
52AA33 - 4933 - 49
62AA81 - 11081 - 110
73BB2 - 72 - 7
83BB19 - 3219 - 32
93BB50 - 8050 - 80
104BB8 - 188 - 18
114BB33 - 4933 - 49
124BB81 - 11081 - 110

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