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- PDB-3m88: Crystal structure of the cysteine protease inhibitor, EhICP2, fro... -

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Basic information

Entry
Database: PDB / ID: 3m88
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: 1.9 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)25,3165
Polymers25,1492
Non-polymers1673
Water2,144119
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)12,7063
Polymers12,5741
Non-polymers1322
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1370 Å2
ΔGint-35 kcal/mol
Surface area11830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.041, 60.507, 60.660
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121

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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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Ammonium sulfate; 30% PEG 8000; 0.1M Sodium cacodylate, pH 6.5, 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 6, 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: 1.9→30.253 Å / Num. all: 17712 / Num. obs: 17712 / % possible obs: 99.9 % / Observed criterion σ(F): 0.7 / Observed criterion σ(I): 0.7 / Redundancy: 9.5 % / Biso Wilson estimate: 18.8 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→2 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.732 / Mean I/σ(I) obs: 5.4 / Num. unique all: 2525 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 41.32 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å30.25 Å
Translation2.5 Å30.25 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: 1.9→30.253 Å / Occupancy max: 1 / Occupancy min: 0.42 / SU ML: 0.23 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 1.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1222 6.91 %RANDOM
Rwork0.185 ---
obs0.188 17679 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.273 Å2 / ksol: 0.345 e/Å3
Displacement parametersBiso max: 121.87 Å2 / Biso mean: 32.659 Å2 / Biso min: 9.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.425 Å20 Å2-0 Å2
2--4.823 Å20 Å2
3----5.248 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30.253 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1630 0 7 119 1756
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061697
X-RAY DIFFRACTIONf_angle_d1.1072317
X-RAY DIFFRACTIONf_chiral_restr0.08270
X-RAY DIFFRACTIONf_plane_restr0.005293
X-RAY DIFFRACTIONf_dihedral_angle_d12.328601
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 (%)
1.9-1.9760.2721350.207178319181783100
1.976-2.0660.2251370.19179619331796100
2.066-2.1750.2561290.18182019491820100
2.175-2.3110.2331260.178179819241798100
2.311-2.490.2361410.192181019511810100
2.49-2.740.2381250.194183819631838100
2.74-3.1360.2641400.184182719671827100
3.136-3.950.2051270.163185819851858100
3.95-30.2570.1961620.18719272089192799
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)
16.0102-1.0735-1.31911.12940.55942.42910.17911.0116-0.29660.1435-0.13790.04160.339-0.4441-0.00460.0735-0.01240.0270.2032-0.01510.146218.1068-16.154-3.2215
22.86010.8570.75831.92651.43852.8093-0.04090.2412-0.3029-0.11280.0592-0.2353-0.08430.06810.00080.1263-0.06380.00060.07950.02570.140529.8115-12.81711.4126
33.35370.9491.68991.89072.28653.3410.0216-0.6903-0.22880.7784-0.11490.93720.152-0.4086-0.18470.52280.0690.1710.160.07120.205525.6688-0.05029.0336
47.7243-2.05713.91851.0773-1.52222.4205-0.0122-0.73690.29060.24320.23740.4103-0.9987-0.685-0.65090.4181-0.04210.0680.0670.02720.115929.3328-1.650811.8554
51.20730.514-0.74272.68390.70122.5049-0.02530.1771-0.1643-0.10150.0267-0.4067-0.05490.46080.00060.072-0.03810.03140.0956-0.00650.157635.1026-15.38710.6566
61.39430.7475-0.53061.85530.46190.58420.1946-0.1259-0.0105-0.062-0.3715-0.1581-0.15640.0156-0.00160.08170.00720.01680.2366-0.01190.121713.1496-15.4771-2.8834
71.1379-0.0438-0.55882.26290.33820.32160.21930.3369-0.1574-0.2305-0.3848-0.11730.12360.28160.00020.090.05690.00870.27370.0150.14657.7183-16.7344-3.7356
81.8821-0.14570.57942.6471.61732.30340.02970.22710.09970.2356-0.08320.2431-0.4274-0.10760.00330.09380.07110.00440.1730.0150.10910.262-6.6886-4.0017
90.7380.17470.06411.1387-0.01421.1880.11210.1416-0.07210.2439-0.25050.4512-0.1756-0.10970.00330.13120.07760.02520.1402-0.03560.1714-2.957-14.3938-2.9274
101.94221.4257-0.46622.1470.61721.7950.03920.55740.0968-0.1995-0.15980.5258-0.3561-0.1724-0.04290.09030.0931-0.03690.157-0.04720.1414-2.4604-17.2234-8.2856
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid -3:21)A-3 - 21
2X-RAY DIFFRACTION2(chain A and resid 22:65)A22 - 65
3X-RAY DIFFRACTION3(chain A and resid 66:76)A66 - 76
4X-RAY DIFFRACTION4(chain A and resid 77:85)A77 - 85
5X-RAY DIFFRACTION5(chain A and resid 86:123)A86 - 123
6X-RAY DIFFRACTION6(chain B and resid -4:24)B-4 - 24
7X-RAY DIFFRACTION7(chain B and resid 25:44)B25 - 44
8X-RAY DIFFRACTION8(chain B and resid 45:88)B45 - 88
9X-RAY DIFFRACTION9(chain B and resid 89:106)B89 - 106
10X-RAY DIFFRACTION10(chain B and resid 107:123)B107 - 123

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