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- PDB-6qsb: Crystal Structure of Arg470His mutant of Human Prolidase with Mn ions -

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Basic information

Entry
Database: PDB / ID: 6qsb
TitleCrystal Structure of Arg470His mutant of Human Prolidase with Mn ions
ComponentsXaa-Pro dipeptidase
KeywordsHYDROLASE / Metal binding / dipeptidase / mutation
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
: / Xaa-Pro dipeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.99 Å
AuthorsWilk, P. / Wator, E. / Weiss, M.S.
CitationJournal: Genet Mol Biol / Year: 2021
Title: Structural analysis of new compound heterozygous variants in PEPD gene identified in a patient with Prolidase Deficiency diagnosed by exome sequencing.
Authors: Linhares, N.D. / Wilk, P. / Wator, E. / Tostes, M.A. / Weiss, M.S. / Pena, S.D.J.
History
DepositionFeb 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 1.2Mar 6, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,05613
Polymers109,1922
Non-polymers86411
Water14,034779
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-58 kcal/mol
Surface area35260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.555, 108.533, 211.804
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-813-

HOH

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Components

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


Mass: 54595.996 Da / Num. of mol.: 2 / Mutation: R470H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEPD, PRD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P12955, Xaa-Pro dipeptidase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / 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.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 779 / 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: 2.77 Å3/Da / Density % sol: 55.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 10mM NaTetraBorate, 690-760mM NaCitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 5, 2018
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.99→48.3 Å / Num. obs: 81795 / % possible obs: 99.7 % / Redundancy: 6.87 % / Biso Wilson estimate: 34.08 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.34 / Rrim(I) all: 0.368 / Net I/σ(I): 5.43
Reflection shellResolution: 1.99→2.11 Å / Redundancy: 7.01 % / Rmerge(I) obs: 2.842 / Mean I/σ(I) obs: 0.63 / Num. unique obs: 12976 / CC1/2: 0.235 / Rrim(I) all: 3.067 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.05 Å48.3 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASER2.8.1phasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M4Q

5m4q


Resolution: 1.99→23.366 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 25.58
RfactorNum. reflection% reflection
Rfree0.2232 2097 2.57 %
Rwork0.1883 --
obs0.1891 81666 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 127.36 Å2 / Biso mean: 43.0725 Å2 / Biso min: 21.5 Å2
Refinement stepCycle: final / Resolution: 1.99→23.366 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7488 0 97 779 8364
Biso mean--67.33 41.31 -
Num. residues----962
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9887-2.0350.41461350.36185137527298
2.035-2.08580.35391400.323552845424100
2.0858-2.14220.33061380.304652495387100
2.1422-2.20520.35141390.28952835422100
2.2052-2.27630.31781390.271252625401100
2.2763-2.35760.29431390.258852885427100
2.3576-2.45190.28811390.237452535392100
2.4519-2.56330.2891390.231652975436100
2.5633-2.69830.2781400.21852965436100
2.6983-2.86710.24741390.201153005439100
2.8671-3.0880.20541410.181253205461100
3.088-3.39790.21221400.163453455485100
3.3979-3.88760.18281410.136353565497100
3.8876-4.89060.13491430.121353965539100
4.8906-23.36760.18721450.17425503564899

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