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- PDB-3fnu: Crystal structure of KNI-10006 bound histo-aspartic protease (HAP... -

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Basic information

Entry
Database: PDB / ID: 3fnu
TitleCrystal structure of KNI-10006 bound histo-aspartic protease (HAP) from Plasmodium falciparum
ComponentsHAP protein
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Histo-aspartic protease / HYDROLASE / Plasmepsin / Aspartic protease / KNI / KNI-10006 / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


MHC class II antigen presentation / plasmepsin II / acquisition of nutrients from host / vacuolar lumen / Neutrophil degranulation / food vacuole / aspartic-type endopeptidase activity / lysosome / proteolysis / membrane
Similarity search - Function
Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
KNI-10006 / Chem-006 / Plasmepsin III
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBhaumik, P. / Gustchina, A. / Wlodawer, A.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structures of the histo-aspartic protease (HAP) from Plasmodium falciparum.
Authors: Bhaumik, P. / Xiao, H. / Parr, C.L. / Kiso, Y. / Gustchina, A. / Yada, R.Y. / Wlodawer, A.
History
DepositionDec 26, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Feb 27, 2013Group: Other
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: HAP protein
B: HAP protein
C: HAP protein
D: HAP protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,2688
Polymers149,7414
Non-polymers2,5274
Water1,71195
1
A: HAP protein
B: HAP protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1344
Polymers74,8712
Non-polymers1,2642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2820 Å2
ΔGint-23 kcal/mol
Surface area28700 Å2
MethodPISA
2
C: HAP protein
D: HAP protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,1344
Polymers74,8712
Non-polymers1,2642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2800 Å2
ΔGint-26 kcal/mol
Surface area28580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.100, 166.100, 276.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ASN / End label comp-ID: ASN / Refine code: 1 / Auth seq-ID: 0 - 327 / Label seq-ID: 6 - 331

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12CC
22DD

NCS ensembles :
ID
1
2
DetailsFour molecules of histo-aspartic protease (HAP) are present in the asymmetric unit. These four molecules are present as two dimers. Each protein molecule is complexed to one KNI-10006 molecule.

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Components

#1: Protein
HAP protein


Mass: 37435.250 Da / Num. of mol.: 4 / Fragment: Histo-aspartic protease
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: HAP, PF14_0078 / Plasmid: pET32b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3)pLysS / References: UniProt: Q8IM15
#2: Chemical
ChemComp-006 / (4R)-3-[(2S,3S)-3-{[(2,6-dimethylphenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide / KNI-10006


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 631.782 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C35H41N3O6S / References: KNI-10006
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / 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

CrystalDensity Matthews: 3.19 Å3/Da / Density % sol: 61.42 %
Description: AUTHORS STATE THAT THE VALUE OF RMERGE IN THE HIGHEST RESOLUTION SHELL IS HIGH DUE TO POORLY DIFFRACTING CRYSTAL/HIGH SYMMETRY SPACE GROUP/HIGHLY REDUNDANT DATA. CRYSTAL HAS SUFFERED SOME RADIATION DAMAGE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M KH2PO4, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.99999 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. all: 39071 / Num. obs: 39041 / % possible obs: 99.9 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.128
Reflection shellResolution: 3→3.1 Å / Redundancy: 14.1 % / Rmerge(I) obs: 1.642 / Mean I/σ(I) obs: 1.7 / Num. unique all: 3590 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.4.0057refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.932 / SU B: 44.709 / SU ML: 0.38 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.415 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1950 5 %RANDOM
Rwork0.222 ---
obs0.223 37061 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.564 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å20 Å20 Å2
2---0.69 Å20 Å2
3---1.39 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10392 0 180 95 10667
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02210856
X-RAY DIFFRACTIONr_angle_refined_deg1.41.98314756
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.25451300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31825.583480
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.371151820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6551512
X-RAY DIFFRACTIONr_chiral_restr0.1020.21636
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218192
X-RAY DIFFRACTIONr_mcbond_it0.321.56532
X-RAY DIFFRACTIONr_mcangle_it0.635210664
X-RAY DIFFRACTIONr_scbond_it0.87734324
X-RAY DIFFRACTIONr_scangle_it1.6164.54092
Refine LS restraints NCS

Dom-ID: 1 / Number: 2598 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.040.05
2Ctight positional0.030.05
1Atight thermal0.060.5
2Ctight thermal0.050.5
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 141 -
Rwork0.349 2687 -
obs--100 %
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)
17.547-1.8285-1.76723.16460.49383.89350.11440.70610.1737-0.3194-0.01120.1285-0.1777-0.4819-0.10320.4083-0.1583-0.00020.2174-0.01390.1934-12.198-55.28-86.915
27.97912.03290.51066.35232.20655.4480.1374-0.43751.24870.3839-0.01090.2152-0.35220.5937-0.12640.3627-0.0060.15350.255-0.17510.401611.87-50.77-81.596
33.70171.46740.3418.7331-0.03894.31220.1723-0.4227-0.18790.4646-0.18020.03860.1824-0.4370.0080.27450.01110.00860.1721-0.06740.1546-9.602-27.672-53.112
47.68260.2644-2.85076.51592.87717.5783-0.27191.0224-0.2595-1.7250.0036-0.4182-0.6947-0.0840.26820.86210.01060.12230.07820.05560.35760.036-16.916-73.592
56.166-1.99661.26837.2331-3.019.6031-0.6348-0.53660.18110.86671.26010.9218-0.5237-1.2614-0.62520.80040.48590.37591.08690.16520.613-6.731-33.278-13.171
67.7555-2.1233-0.104211.5288-0.49776.9277-0.4241-0.5044-0.04750.80720.4156-1.0226-0.4580.54170.00851.04060.354-0.04380.9491-0.02050.360813.626-44.822-4.693
74.4551-1.4783-0.78479.21362.31635.53340.0138-0.3471.1930.0580.2575-1.4815-0.77650.3465-0.27140.43260.03360.13570.57380.1770.827325.65-29.68-42.303
89.99430.1453-2.95998.5442-0.96128.6068-0.249-1.0816-0.40310.97250.02130.29730.306-0.22650.22760.39120.18850.14780.50830.01450.30318.491-53.408-40.156
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 194
2X-RAY DIFFRACTION2A195 - 327
3X-RAY DIFFRACTION3B0 - 194
4X-RAY DIFFRACTION4B195 - 327
5X-RAY DIFFRACTION5C0 - 194
6X-RAY DIFFRACTION6C195 - 327
7X-RAY DIFFRACTION7D0 - 194
8X-RAY DIFFRACTION8D195 - 327

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