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- PDB-3m86: Crystal structure of the cysteine protease inhibitor, EhICP2, fro... -

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Basic information

Entry
Database: PDB / ID: 3m86
TitleCrystal structure of the cysteine protease inhibitor, EhICP2, from Entamoeba histolytica
ComponentsAmoebiasin-2
KeywordsPROTEIN BINDING / cysteine protease inhibitor / Protease
Function / homology
Function and homology information


cysteine-type endopeptidase inhibitor activity / phagocytic vesicle / lysosome / enzyme binding
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 speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.65 Å
AuthorsLara-Gonzalez, S. / Casados-Vazquez, L.E. / Brieba, L.G.
CitationJournal: Gene / Year: 2011
Title: Crystal structure of the cysteine protease inhibitor 2 from Entamoeba histolytica: functional convergence of a common protein fold.
Authors: Casados-Vazquez, L.E. / Lara-Gonzalez, S. / Brieba, L.G.
History
DepositionMar 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Amoebiasin-2
B: Amoebiasin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6507
Polymers25,1492
Non-polymers5015
Water3,369187
1
A: Amoebiasin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,6102
Polymers12,5741
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Amoebiasin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,0405
Polymers12,5741
Non-polymers4664
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Amoebiasin-2
B: Amoebiasin-2
hetero molecules

A: Amoebiasin-2
B: Amoebiasin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,30014
Polymers50,2984
Non-polymers1,00310
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555x,-y,-z1
Buried area6070 Å2
ΔGint-125 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.523, 60.122, 61.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-152-

HOH

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Components

#1: Protein Amoebiasin-2 / Cysteine protease inhibitor 2 / EhICP2 / ICP-2


Mass: 12574.416 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Strain: HM-1:IMSS / Gene: EHI_040460, ICP2 / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta-gami / References: UniProt: C4M2H5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Lithium sulfate; 30% PEG4000; 0.1M Tris, pH 8.5, vapor diffusion, hanging drop, temperature 294.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.078 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 5, 2009
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 1.65→28.262 Å / Num. all: 25606 / Num. obs: 25606 / % possible obs: 99.3 % / Observed criterion σ(F): 1.12 / Observed criterion σ(I): 1.12 / Redundancy: 8.8 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 23.3
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 8.9 % / Rmerge(I) obs: 0.162 / Mean I/σ(I) obs: 10.3 / Num. unique all: 3652 / % possible all: 98.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.44 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.26 Å
Translation2.5 Å28.26 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NNR

2nnr


Resolution: 1.65→27.324 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.19 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 1.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.214 1285 5.02 %RANDOM
Rwork0.183 ---
all0.185 25579 --
obs0.185 25579 99.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.323 Å2 / ksol: 0.401 e/Å3
Displacement parametersBiso max: 129.56 Å2 / Biso mean: 25.184 Å2 / Biso min: 6.35 Å2
Baniso -1Baniso -2Baniso -3
1-2.257 Å2-0 Å2-0 Å2
2---0.308 Å20 Å2
3----1.949 Å2
Refinement stepCycle: LAST / Resolution: 1.65→27.324 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1667 0 28 187 1882
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061801
X-RAY DIFFRACTIONf_angle_d1.0992463
X-RAY DIFFRACTIONf_chiral_restr0.075285
X-RAY DIFFRACTIONf_plane_restr0.005312
X-RAY DIFFRACTIONf_dihedral_angle_d12.901661
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.65-1.7160.2131360.17726452781264598
1.716-1.7940.2211430.16926192762261999
1.794-1.8890.2291410.16626532794265399
1.889-2.0070.2011380.16526702808267099
2.007-2.1620.21320.16726732805267399
2.162-2.3790.2021350.1727172852271799
2.379-2.7230.221490.192271028592710100
2.723-3.430.231530.182275329062753100
3.43-27.3280.1971580.19228543012285499
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)
11.4078-0.6163-1.12523.98444.09244.5023-0.1234-0.4917-0.17860.1935-0.14060.25770.3597-0.2549-0.38950.0540.0315-0.02320.18980.00890.0934-40.494516.03954.2718
20.8378-0.3750.2611.81520.13622.30370.1013-0.00240.0626-0.1534-0.0765-0.121-0.1502-0.1689-0.00030.0510.02730.01380.06440.01870.0793-29.340113.6903-3.4468
30.2116-0.32170.05310.62640.35041.3291-0.1283-0.0240.13460.13790.2058-0.5415-0.0710.4577-0.0150.13970.0754-0.0620.143-0.07740.1219-23.864412.72337.51
40.2534-0.1218-0.49490.7911-0.04631.23560.07330.2697-0.0216-0.2064-0.0550.27150.0203-0.4914-0.0010.172-0.0127-0.01710.1021-0.00750.0755-30.67342.1111-1.4005
50.0875-0.05870.04720.0639-0.04740.0355-0.18190.04290.2072-0.0281-0.55410.118-0.1335-0.0222-0.00321.7750.2874-0.4971.3046-0.13571.2116-33.5268-0.7383-18.5133
61.28860.1965-0.80951.29770.41221.8074-0.1090.03460.06730.1408-0.07720.08080.4413-0.2663-0.01150.09410.0209-0.02570.07730.00720.0792-29.89099.62511.3561
71.2922-0.1781-0.03672.57270.00232.67280.2763-0.24850.2796-0.18520.2008-0.7463-0.33540.48390.04590.0239-0.01320.02820.0818-0.04120.1677-20.302715.3869-3.3384
81.0744-0.70420.36941.77560.33330.44550.10170.21570.19820.06050.0053-0.0330.0237-0.2019-0.00060.05510.0093-0.01590.1015-0.00340.072711.359415.82172.8317
90.91920.5094-0.21661.2233-0.33321.4550.1118-0.12440.03790.09-0.15650.15670.03160.01280.00020.07510.00370.00270.0919-0.00370.10622.635812.73235.2177
100.06220.0117-0.03460.0197-0.04710.1085-0.2307-0.10190.0342-0.28270.12110.15820.167-0.41440.00160.1201-0.0613-0.04950.2030.04520.1674-4.44815.7755-4.111
110.73090.1973-0.64220.81010.26170.8123-0.1798-0.1564-0.03370.1244-0.0003-0.04140.1680.03390.00020.11940.0204-0.0120.07720.02180.06783.39845.9024-0.4905
121.40310.81-0.3941.78850.00312.20420.0011-0.1111-0.1078-0.0421-0.02120.13410.3129-0.00410.00040.0470.0045-0.0140.04650.00320.0550.237711.33072.5609
130.5640.39151.26660.33590.47375.4331-0.20520.59160.344-0.73220.5165-0.34690.95210.38550.00270.3585-0.1014-0.04460.33090.06410.594-17.4914.59659.4645
141.0453-0.6690.3751.22640.03350.52980.119-0.22290.39740.20790.09110.3338-0.1542-0.00880.00110.1052-0.00410.01450.0892-0.01220.0875-0.685219.04046.0458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -4:21)A-4 - 21
2X-RAY DIFFRACTION2(chain A and resid 22:52)A22 - 52
3X-RAY DIFFRACTION3(chain A and resid 53:63)A53 - 63
4X-RAY DIFFRACTION4(chain A and resid 64:70)A64 - 70
5X-RAY DIFFRACTION5(chain A and resid 71:79)A71 - 79
6X-RAY DIFFRACTION6(chain A and resid 80:94)A80 - 94
7X-RAY DIFFRACTION7(chain A and resid 95:123)A95 - 123
8X-RAY DIFFRACTION8(chain B and resid -4:24)B-4 - 24
9X-RAY DIFFRACTION9(chain B and resid 25:53)B25 - 53
10X-RAY DIFFRACTION10(chain B and resid 54:59)B54 - 59
11X-RAY DIFFRACTION11(chain B and resid 60:71)B60 - 71
12X-RAY DIFFRACTION12(chain B and resid 72:104)B72 - 104
13X-RAY DIFFRACTION13(chain B and resid 105:111)B105 - 111
14X-RAY DIFFRACTION14(chain B and resid 112:123)B112 - 123

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