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- PDB-5jr6: The Xray Crystal Structure of P. falciparum Aminopeptidase P in C... -

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Basic information

Entry
Database: PDB / ID: 5jr6
TitleThe Xray Crystal Structure of P. falciparum Aminopeptidase P in Complex With Apstatin
Components
  • Apstatin
  • Peptidase, putative
KeywordsHYDROLASE / Aminopeptidase
Function / homologyCreatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Alpha-Beta Complex / Alpha Beta / APSTATIN / : / PHOSPHATE ION / :
Function and homology information
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDrinkwater, N. / McGowan, S.
CitationJournal: Biochem.J. / Year: 2016
Title: Structure and substrate fingerprint of aminopeptidase P from Plasmodium falciparum.
Authors: Drinkwater, N. / Sivaraman, K.K. / Bamert, R.S. / Rut, W. / Mohamed, K. / Vinh, N.B. / Scammells, P.J. / Drag, M. / McGowan, S.
History
DepositionMay 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2016Group: Database references
Revision 1.2Oct 26, 2016Group: Structure summary
Revision 1.3Sep 27, 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 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptidase, putative
B: Peptidase, putative
F: Apstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,0998
Polymers154,7843
Non-polymers3155
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-58 kcal/mol
Surface area47980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.220, 99.930, 105.170
Angle α, β, γ (deg.)90.00, 105.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peptidase, putative


Mass: 77162.922 Da / Num. of mol.: 2 / Fragment: UNP residues 108-764
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF14_0517 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IKT5
#2: Protein/peptide Apstatin


Type: Peptide-like / Class: Enzyme inhibitor / Mass: 458.530 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: APSTATIN
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.41 Å3/Da / Density % sol: 48.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 45% MPD, 0.1M sodium cacodylate pH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→71.03 Å / Num. obs: 65055 / % possible obs: 99.6 % / Redundancy: 3.7 % / Net I/σ(I): 8.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JQK

5jqk


Resolution: 2.3→42.793 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 3236 4.98 %
Rwork0.1965 --
obs0.1988 65020 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→42.793 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9012 0 9 193 9214
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089196
X-RAY DIFFRACTIONf_angle_d1.16912488
X-RAY DIFFRACTIONf_dihedral_angle_d13.9263236
X-RAY DIFFRACTIONf_chiral_restr0.0471439
X-RAY DIFFRACTIONf_plane_restr0.0071595
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.33430.33641490.282673X-RAY DIFFRACTION100
2.3343-2.37080.2991290.26852637X-RAY DIFFRACTION100
2.3708-2.40970.28231310.25162744X-RAY DIFFRACTION100
2.4097-2.45120.28351310.25132672X-RAY DIFFRACTION100
2.4512-2.49580.3131440.24042678X-RAY DIFFRACTION100
2.4958-2.54380.30281400.2442697X-RAY DIFFRACTION100
2.5438-2.59570.2991350.23542657X-RAY DIFFRACTION100
2.5957-2.65210.30841430.23362678X-RAY DIFFRACTION100
2.6521-2.71380.29561440.23172669X-RAY DIFFRACTION100
2.7138-2.78170.26121370.2192720X-RAY DIFFRACTION100
2.7817-2.85690.26291300.21282673X-RAY DIFFRACTION100
2.8569-2.94090.29761410.22082668X-RAY DIFFRACTION100
2.9409-3.03580.27111310.20652689X-RAY DIFFRACTION100
3.0358-3.14430.26131330.20932712X-RAY DIFFRACTION100
3.1443-3.27010.24461350.19712675X-RAY DIFFRACTION100
3.2701-3.41890.27221350.19282705X-RAY DIFFRACTION99
3.4189-3.59910.21851390.18162676X-RAY DIFFRACTION100
3.5991-3.82440.20511740.16842670X-RAY DIFFRACTION100
3.8244-4.11950.19311500.16352673X-RAY DIFFRACTION100
4.1195-4.53360.1991580.15892702X-RAY DIFFRACTION100
4.5336-5.18870.21921390.16812692X-RAY DIFFRACTION99
5.1887-6.53350.22491580.21052662X-RAY DIFFRACTION98
6.5335-42.80010.25631300.19622762X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -24.5105 Å / Origin y: 58.7471 Å / Origin z: 232.5463 Å
111213212223313233
T0.3282 Å20.0791 Å2-0.0102 Å2-0.4042 Å2-0.1454 Å2--0.3395 Å2
L2.77 °2-0.5133 °20.6567 °2-1.1168 °2-0.0927 °2--0.856 °2
S0.2561 Å °0.6756 Å °-0.5184 Å °-0.1164 Å °-0.1232 Å °0.0894 Å °0.0956 Å °-0.044 Å °-0.0361 Å °
Refinement TLS groupSelection details: all

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