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- PDB-4s2t: Crystal structure of X-prolyl aminopeptidase from Caenorhabditis ... -

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Basic information

Entry
Database: PDB / ID: 4s2t
TitleCrystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: a cytosolic enzyme with a di-nuclear active site
Components
  • Protein APP-1
  • apstatin
KeywordsHydrolase/hydrolase inhibitor / pitta-bread fold / metalloprotease / zinc binding / Hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


Xaa-Pro aminopeptidase / metalloaminopeptidase activity / : / protein homodimerization activity / proteolysis / zinc ion binding / cytoplasm
Similarity search - Function
Peptidase M24, C-terminal domain / Aminopeptidase P / : / C-terminal region of peptidase_M24 / Creatinase/Prolidase N-terminal domain / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal ...Peptidase M24, C-terminal domain / Aminopeptidase P / : / C-terminal region of peptidase_M24 / Creatinase/Prolidase N-terminal domain / Creatinase, N-terminal / Creatinase/Prolidase N-terminal domain / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
APSTATIN / Xaa-Pro aminopeptidase app-1
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsIyer, S. / La-Borde, P. / Payne, K.A.P. / Parsons, M.R. / Turner, A.J. / Isaac, R.E. / Acharya, K.R.
CitationJournal: FEBS Open Bio / Year: 2015
Title: Crystal structure of X-prolyl aminopeptidase from Caenorhabditis elegans: A cytosolic enzyme with a di-nuclear active site.
Authors: Iyer, S. / La-Borde, P.J. / Payne, K.A. / Parsons, M.R. / Turner, A.J. / Isaac, R.E. / Acharya, K.R.
History
DepositionJan 22, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: Protein APP-1
Q: Protein APP-1
A: apstatin
B: apstatin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,27915
Polymers145,3444
Non-polymers93411
Water6,341352
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7630 Å2
ΔGint-308 kcal/mol
Surface area46590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.590, 86.810, 113.130
Angle α, β, γ (deg.)90.00, 115.96, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11P
21Q

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 1 - 616 / Label seq-ID: 24 - 639

Dom-IDAuth asym-IDLabel asym-ID
1PA
2QB

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Components

#1: Protein Protein APP-1


Mass: 72213.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: app-1, CELE_W03G9.4, W03G9.4 / Plasmid: pET19b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon-Plus (DE3)-RIL / References: UniProt: O44750
#2: Protein/peptide apstatin


Type: Peptide-like / Class: Enzyme inhibitor / Mass: 458.530 Da / Num. of mol.: 2 / Source method: obtained synthetically / References: APSTATIN
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 42.76 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M sodium iodide, 0.1 M Bis-Tris propane, pH 7.5, 20 % w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.968 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 13, 2013
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 2.15→38.52 Å / Num. all: 61133 / Num. obs: 61133 / % possible obs: 91.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.6 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.3
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.453 / Mean I/σ(I) obs: 2.4 / % possible all: 60.4

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.8.0073refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: native C. elegans APP-1 structure

Resolution: 2.15→38.52 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 7.211 / SU ML: 0.18 / Cross valid method: THROUGHOUT / ESU R: 0.352 / ESU R Free: 0.233 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 3099 5.1 %RANDOM
Rwork0.20451 ---
obs0.20668 58022 91.7 %-
all-61133 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.227 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20.01 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.15→38.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9799 0 39 352 10190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910015
X-RAY DIFFRACTIONr_bond_other_d0.0030.029460
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.96213592
X-RAY DIFFRACTIONr_angle_other_deg0.8763.00221789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.63351223
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84724.241448
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.187151688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1651548
X-RAY DIFFRACTIONr_chiral_restr0.0690.21519
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211214
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022285
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7683.4214910
X-RAY DIFFRACTIONr_mcbond_other1.7683.4214910
X-RAY DIFFRACTIONr_mcangle_it2.7925.1236127
X-RAY DIFFRACTIONr_mcangle_other2.8485.1886158
X-RAY DIFFRACTIONr_scbond_it2.1673.6625105
X-RAY DIFFRACTIONr_scbond_other2.1393.6395022
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3255.3577357
X-RAY DIFFRACTIONr_long_range_B_refined5.00327.57911479
X-RAY DIFFRACTIONr_long_range_B_other5.00327.58111480
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 38621 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1P
2Q
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 160 -
Rwork0.291 2792 -
obs--60.39 %

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