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- PDB-4it7: Crystal structure of Al-CPI -

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Basic information

Entry
Database: PDB / ID: 4it7
TitleCrystal structure of Al-CPI
ComponentsCPI
KeywordsHYDROLASE INHIBITOR / CPI / cystatin
Function / homology
Function and homology information


cysteine-type endopeptidase inhibitor activity / vesicle / extracellular space / cytoplasm
Similarity search - Function
Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesAscaris lumbricoides (common roundworm)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMei, G.Q. / Liu, S.L. / Sun, M.Z. / Liu, J.
CitationJournal: Plos One / Year: 2014
Title: Structural Basis for the Immunomodulatory Function of Cysteine Protease Inhibitor from Human Roundworm Ascaris lumbricoides.
Authors: Mei, G. / Dong, J. / Li, Z. / Liu, S. / Liu, Y. / Sun, M. / Liu, G. / Su, Z. / Liu, J.
History
DepositionJan 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2014Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CPI
B: CPI
C: CPI
D: CPI


Theoretical massNumber of molelcules
Total (without water)48,1834
Polymers48,1834
Non-polymers00
Water2,270126
1
A: CPI


Theoretical massNumber of molelcules
Total (without water)12,0461
Polymers12,0461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CPI


Theoretical massNumber of molelcules
Total (without water)12,0461
Polymers12,0461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CPI


Theoretical massNumber of molelcules
Total (without water)12,0461
Polymers12,0461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: CPI


Theoretical massNumber of molelcules
Total (without water)12,0461
Polymers12,0461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.510, 44.499, 44.582
Angle α, β, γ (deg.)90.000, 89.990, 90.000
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CPI / cysteine protease inhibitor


Mass: 12045.677 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ascaris lumbricoides (common roundworm)
Gene: cpi / Production host: Escherichia coli (E. coli) / References: UniProt: E9N3T6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 0.2 M sodium acetate trihydrate, 0.1 M sodium cacodylate trihydrate, 30% w/v polyethylene glycol, pH 6.5, vapor diffusion, temperature 293K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.9792
SEALED TUBEOXFORD DIFFRACTION ENHANCE ULTRA21.54056
DetectorDetector: CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97921
21.540561
ReflectionResolution: 2.1→44.58 Å / Num. obs: 19288 / % possible obs: 98.8 %

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→18.01 Å / Cor.coef. Fo:Fc: 0.957 / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0 / ESU R: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflection
Rfree0.2565 988 -
Rwork0.2035 --
obs0.2035 19288 98.83 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 101.86 Å2 / Biso mean: 49.105 Å2 / Biso min: 23.02 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0.14 Å2-0.01 Å2
2--2.68 Å20.01 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 2.1→18.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3220 0 0 126 3346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.023264
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.9494428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7325424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg48.49127.188128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.14915596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.867158
X-RAY DIFFRACTIONr_chiral_restr0.1220.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212364
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.322 1433 -
obs--99.86 %

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