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- PDB-5mc0: Crystal Structure of delTyr231 mutant of Human Prolidase with Mn ... -

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Basic information

Entry
Database: PDB / ID: 5mc0
TitleCrystal Structure of delTyr231 mutant of Human Prolidase with Mn ions and GlyPro ligand
ComponentsXaa-Pro dipeptidase
KeywordsHYDROLASE / prolidase / peptidase / hydrolysis / pita-bread / metalloenzyme / mutation
Function / homology
Function and homology information


Xaa-Pro dipeptidase / proline dipeptidase activity / amino acid metabolic process / negative regulation of programmed cell death / metalloaminopeptidase activity / collagen catabolic process / metallocarboxypeptidase activity / peptidase activity / manganese ion binding / proteolysis / extracellular exosome
Similarity search - Function
Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / : / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Creatine Amidinohydrolase ...Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / : / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / 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
GLYCINE / : / HYDROXIDE ION / PROLINE / Xaa-Pro dipeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.56 Å
AuthorsWilk, P. / Mueller, U. / Dobbek, H. / Weiss, M.S.
CitationJournal: FEBS J. / Year: 2018
Title: Structural basis for prolidase deficiency disease mechanisms.
Authors: Wilk, P. / Uehlein, M. / Piwowarczyk, R. / Dobbek, H. / Mueller, U. / Weiss, M.S.
History
DepositionNov 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.4Jan 17, 2024Group: 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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.ptnr2_symmetry
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xaa-Pro dipeptidase
B: Xaa-Pro dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,49428
Polymers106,5812
Non-polymers1,91326
Water22,4111244
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9400 Å2
ΔGint-73 kcal/mol
Surface area35310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.943, 108.113, 211.927
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND SEGID
211CHAIN B AND SEGID

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Xaa-Pro dipeptidase / X-Pro dipeptidase / Imidodipeptidase / Peptidase D / Proline dipeptidase / Prolidase


Mass: 53290.531 Da / Num. of mol.: 2 / Mutation: delY231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEPD, PRD / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Rosetta / References: UniProt: P12955, Xaa-Pro dipeptidase

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Non-polymers , 8 types, 1270 molecules

#2: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#4: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2 / Source: (synth.) Homo sapiens (human)
#5: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2 / Source: (synth.) Homo sapiens (human)
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1244 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.78 Å3/Da / Density % sol: 55.82 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 7.4 / Details: 10mM NaBorate, 640mM NaCitrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 18, 2014
RadiationMonochromator: Double Crystal Monochromator Si-11 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.558→48.153 Å / Num. obs: 168926 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.36 % / Biso Wilson estimate: 19.38 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.04
Reflection shellResolution: 1.56→1.65 Å / Rmerge(I) obs: 0.979 / Mean I/σ(I) obs: 1.77 / % possible all: 98.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassification
PHENIXrefinement
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
XSCALEdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M4J

5m4j


Resolution: 1.56→43.26 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 14.47
RfactorNum. reflection% reflection
Rfree0.153 8446 5 %
Rwork0.116 --
obs0.118 168912 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.12 Å2
Refinement stepCycle: LAST / Resolution: 1.56→43.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7452 0 111 1244 8807
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098012
X-RAY DIFFRACTIONf_angle_d1.21310866
X-RAY DIFFRACTIONf_dihedral_angle_d13.7963018
X-RAY DIFFRACTIONf_chiral_restr0.0531174
X-RAY DIFFRACTIONf_plane_restr0.0061425
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A16X-RAY DIFFRACTIONPOSITIONAL
12B16X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.558-1.57580.34942580.29674903X-RAY DIFFRACTION92
1.5758-1.59430.29212840.2525381X-RAY DIFFRACTION100
1.5943-1.61370.25992750.20935239X-RAY DIFFRACTION100
1.6137-1.63420.24162810.18125349X-RAY DIFFRACTION100
1.6342-1.65570.22482790.17075307X-RAY DIFFRACTION100
1.6557-1.67830.21472820.15695345X-RAY DIFFRACTION100
1.6783-1.70230.22712810.14935351X-RAY DIFFRACTION100
1.7023-1.72770.20882770.14855253X-RAY DIFFRACTION100
1.7277-1.75470.21392830.14335374X-RAY DIFFRACTION100
1.7547-1.78350.20152800.13565319X-RAY DIFFRACTION100
1.7835-1.81430.18172800.12715318X-RAY DIFFRACTION100
1.8143-1.84730.16712790.12055304X-RAY DIFFRACTION100
1.8473-1.88280.19042820.11625357X-RAY DIFFRACTION100
1.8828-1.92120.16442830.10845378X-RAY DIFFRACTION100
1.9212-1.9630.15162800.10555329X-RAY DIFFRACTION100
1.963-2.00860.14472800.10055305X-RAY DIFFRACTION100
2.0086-2.05890.14332810.0995340X-RAY DIFFRACTION100
2.0589-2.11450.14042800.09465336X-RAY DIFFRACTION100
2.1145-2.17680.13582830.09435376X-RAY DIFFRACTION100
2.1768-2.2470.13352820.09045344X-RAY DIFFRACTION100
2.247-2.32730.13382830.08925378X-RAY DIFFRACTION100
2.3273-2.42050.13092830.08945379X-RAY DIFFRACTION100
2.4205-2.53070.13442810.09485338X-RAY DIFFRACTION100
2.5307-2.66410.14462850.09885412X-RAY DIFFRACTION100
2.6641-2.83090.14592820.10285370X-RAY DIFFRACTION100
2.8309-3.04950.14662850.10845404X-RAY DIFFRACTION100
3.0495-3.35620.13992850.10835416X-RAY DIFFRACTION100
3.3562-3.84160.13672850.10535429X-RAY DIFFRACTION100
3.8416-4.8390.11892890.10385482X-RAY DIFFRACTION100
4.839-43.27650.16922980.16075650X-RAY DIFFRACTION100

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