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- PDB-6sre: Crystal Structure of Human Prolidase S202F variant expressed in t... -

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Basic information

Entry
Database: PDB / ID: 6sre
TitleCrystal Structure of Human Prolidase S202F variant expressed in the presence of chaperones
ComponentsXaa-Pro dipeptidase
KeywordsHYDROLASE / prolidase / metallopeptidase / pathological variant
Function / homology
Function and homology information


Xaa-Pro dipeptidase / proline dipeptidase activity / negative regulation of programmed cell death / amino acid metabolic process / metalloaminopeptidase activity / collagen catabolic process / metallocarboxypeptidase activity / manganese ion binding / peptidase activity / 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 / Creatinase/methionine aminopeptidase superfamily ...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 / MANGANESE ION, 1 HYDROXYL COORDINATED / : / PROLINE / Xaa-Pro dipeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.39 Å
AuthorsWator, E. / Rutkiewicz, M. / Wilk, P.
CitationJournal: Febs Lett. / Year: 2020
Title: Co-expression with chaperones can affect protein 3D structure as exemplified by loss-of-function variants of human prolidase.
Authors: Wator, E. / Rutkiewicz, M. / Weiss, M.S. / Wilk, P.
History
DepositionSep 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _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.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
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)109,18119
Polymers107,7182
Non-polymers1,46317
Water20,9151161
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8130 Å2
ΔGint-33 kcal/mol
Surface area35740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.725, 106.858, 216.323
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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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: 53859.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEPD, PRD / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Variant (production host): Arctic Express / References: UniProt: P12955, Xaa-Pro dipeptidase

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Non-polymers , 6 types, 1178 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MH2 / MANGANESE ION, 1 HYDROXYL COORDINATED / [MN(OH)]+


Mass: 71.945 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HMnO
#5: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1161 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 55.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 10mM NaBorate, 760mM NaCitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.39→46.765 Å / Num. obs: 239232 / % possible obs: 99.8 % / Redundancy: 7.16 % / Biso Wilson estimate: 25.2 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.097 / Net I/av σ(I): 10.32 / Net I/σ(I): 10.32
Reflection shellResolution: 1.39→1.47 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 0.74 / Num. unique obs: 38067 / CC1/2: 0.401 / Rrim(I) all: 1.756 / % possible all: 98.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M4J

5m4j


Resolution: 1.39→46.765 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.56
RfactorNum. reflection% reflection
Rfree0.1723 2512 1.05 %
Rwork0.1499 --
obs0.1501 239176 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 145.13 Å2 / Biso mean: 31.1077 Å2 / Biso min: 14.05 Å2
Refinement stepCycle: final / Resolution: 1.39→46.765 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7565 0 181 1161 8907
Biso mean--56.87 40.17 -
Num. residues----967
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.39-1.41630.46521340.45511269497
1.4163-1.44520.48721390.40431304499
1.4452-1.47660.35291380.315813036100
1.4766-1.51090.28641390.252413098100
1.5109-1.54870.2541400.216113141100
1.5487-1.59060.2731380.200113056100
1.5906-1.63740.23741390.183713070100
1.6374-1.69030.2121400.171713169100
1.6903-1.75070.21131380.161613069100
1.7507-1.82080.20911400.146113149100
1.8208-1.90360.18021400.135213143100
1.9036-2.0040.18131390.129613163100
2.004-2.12960.13871400.121413166100
2.1296-2.2940.14221390.122113150100
2.294-2.52480.16141410.126813240100
2.5248-2.89010.16511410.133513294100
2.8901-3.6410.13981410.130213314100
3.641-46.7650.14731460.150813668100

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