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- PDB-2anl: X-ray crystal structure of the aspartic protease plasmepsin 4 fro... -

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Basic information

Entry
Database: PDB / ID: 2anl
TitleX-ray crystal structure of the aspartic protease plasmepsin 4 from the malarial parasite plasmodium malariae bound to an allophenylnorstatine based inhibitor
Componentsplasmepsin IV
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Plasmodium parasite / plasmepsin 4 / aspartic protease / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


membrane => GO:0016020 / aspartic-type endopeptidase activity
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, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...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, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
KNI-764 / Chem-JE2 / Plasmepsin
Similarity search - Component
Biological speciesPlasmodium malariae (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsClemente, J.C. / Govindasamy, L. / Madabushi, A. / Fisher, S.Z. / Moose, R.E. / Yowell, C.A. / Hidaka, K. / Kimura, T. / Hayashi, Y. / Kiso, Y. ...Clemente, J.C. / Govindasamy, L. / Madabushi, A. / Fisher, S.Z. / Moose, R.E. / Yowell, C.A. / Hidaka, K. / Kimura, T. / Hayashi, Y. / Kiso, Y. / Agbandje-McKenna, M. / Dame, J.B. / Dunn, B.M. / McKenna, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of the aspartic protease plasmepsin 4 from the malarial parasite Plasmodium malariae bound to an allophenylnorstatine-based inhibitor.
Authors: Clemente, J.C. / Govindasamy, L. / Madabushi, A. / Fisher, S.Z. / Moose, R.E. / Yowell, C.A. / Hidaka, K. / Kimura, T. / Hayashi, Y. / Kiso, Y. / Agbandje-McKenna, M. / Dame, J.B. / Dunn, B.M. / McKenna, R.
History
DepositionAug 11, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software
Revision 1.5Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 295 NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE ... NON-CRYSTALLOGRAPHIC SYMMETRY THE TRANSFORMATIONS PRESENTED ON THE MTRIX RECORDS BELOW DESCRIBE NON-CRYSTALLOGRAPHIC RELATIONSHIPS AMONG ATOMS IN THIS ENTRY. APPLYING THE APPROPRIATE MTRIX TRANSFORMATION TO THE RESIDUES LISTED FIRST WILL YIELD APPROXIMATE COORDINATES FOR THE RESIDUES LISTED SECOND. CHAIN IDENTIFIERS GIVEN AS "?" REFER TO CHAINS FOR WHICH ATOMS ARE NOT FOUND IN THIS ENTRY. APPLIED TO TRANSFORMED TO TRANSFORM CHAIN RESIDUES CHAIN RESIDUES RMSD SSS A 1 .. 327 B 1 .. 327 ? WHERE SSS -> COLUMNS 8-10 OF MTRIX RECORDS REMARK: NULL

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: plasmepsin IV
B: plasmepsin IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,4134
Polymers74,2622
Non-polymers1,1512
Water25214
1
A: plasmepsin IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7072
Polymers37,1311
Non-polymers5761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: plasmepsin IV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7072
Polymers37,1311
Non-polymers5761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.884, 112.579, 90.404
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.408904, -0.912572, -0.003283), (0.912284, -0.408861, 0.0239), (-0.023153, 0.006777, 0.999709)
Vector: 116.80229, 12.99195, 4.22807)

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Components

#1: Protein plasmepsin IV /


Mass: 37130.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium malariae (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: O60990
#2: Chemical ChemComp-JE2 / (4R)-3-{(2S,3S)-2-hydroxy-3-[(3-hydroxy-2-methylbenzoyl)amino]-4-phenylbutanoyl}-5,5-dimethyl-N-(2-methylbenzyl)-1,3-thiazolidine-4-carboxamide / JE-2147 / AG1776 / KNI-764


Type: peptide-like, Peptide-like / Class: Enzyme inhibitor / Mass: 575.718 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H37N3O5S / References: KNI-764
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3.28 Å3/Da / Density % sol: 62.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 0.2 M ammonium sulfate, 15% PEG 4000 + inhibitor, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Details: osmic mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→25 Å / Num. obs: 14334 / % possible obs: 94 % / Rsym value: 0.104

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
MOLREPphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: homology model

Resolution: 3.3→25 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber /
RfactorNum. reflection
Rfree0.298 -
Rwork0.247 -
obs-14334
Refinement stepCycle: LAST / Resolution: 3.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5234 0 82 14 5330
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.1
X-RAY DIFFRACTIONc_angle_deg1.8

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