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- PDB-6qsc: Crystal Structure of Arg470His mutant of Human Prolidase with Mn ... -

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Basic information

Entry
Database: PDB / ID: 6qsc
TitleCrystal Structure of Arg470His mutant of Human Prolidase with Mn ions and GlyPro ligand
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 / 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 / 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 / Resolution: 1.569 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

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)110,65519
Polymers109,1922
Non-polymers1,46317
Water20,3571130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-32 kcal/mol
Surface area35320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.541, 108.714, 211.548
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-975-

HOH

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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: 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

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Non-polymers , 6 types, 1147 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-MH2 / MANGANESE ION, 1 HYDROXYL COORDINATED / [MN(OH)]+


Mass: 71.945 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HMnO
#4: 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
#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.: 1130 / 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: 55.53 %
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: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2018
RadiationMonochromator: KMC-1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.569→48.35 Å / Num. obs: 165436 / % possible obs: 99.8 % / Redundancy: 7.49 % / Biso Wilson estimate: 29.37 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.077 / Net I/σ(I): 16.61
Reflection shellResolution: 1.569→1.66 Å / Redundancy: 7.66 % / Rmerge(I) obs: 1.212 / Mean I/σ(I) obs: 1.47 / Num. unique obs: 26391 / CC1/2: 0.649 / Rrim(I) all: 1.299 / % possible all: 99.3

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Processing

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

5m4q


Resolution: 1.569→48.347 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 17.56
RfactorNum. reflection% reflection
Rfree0.1674 2100 1.27 %
Rwork0.1468 --
obs0.1471 165419 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 201.51 Å2 / Biso mean: 32.5923 Å2 / Biso min: 14.97 Å2
Refinement stepCycle: final / Resolution: 1.569→48.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7495 0 156 1130 8781
Biso mean--52.03 38.38 -
Num. residues----960
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 (%)
1.5694-1.60590.36841360.3146105671070398
1.6059-1.64610.27991400.26931085610996100
1.6461-1.69060.28911380.23721078410922100
1.6906-1.74030.20561400.21631086711007100
1.7403-1.79650.19091390.19671083410973100
1.7965-1.86070.22441390.17941080010939100
1.8607-1.93520.18431400.1621089611036100
1.9352-2.02330.17211390.15141083410973100
2.0233-2.12990.17281400.13611087111011100
2.1299-2.26340.14871400.13121088211022100
2.2634-2.43810.16881400.13081087411014100
2.4381-2.68350.15121400.13521095711097100
2.6835-3.07170.15281410.1391094811089100
3.0717-3.86980.16571420.12931104011182100
3.8698-48.36960.14051460.13591130911455100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2028-0.06740.01160.51070.03810.37980.0308-0.0149-0.0520.04080.02460.05220.0106-0.004700.17050.0166-0.00390.19340.02340.171416.6359.058781.7294
20.60140.0068-0.05440.4855-0.04110.15260.0265-0.01750.0758-0.01480.00920.0045-0.05090.001300.18650.02470.01880.17960.00950.169724.621140.205572.6359
30.00690.0309-0.00830.91420.32880.18390.0066-0.00930.0017-0.00910.0084-0.00380.0032-0.0027-0.00290.26470.0240.00130.29560.00380.317818.748244.037577.5641
40.0526-0.0820.01310.1655-0.02640.0043-0.0120.00260.0033-0.0037-0.00470.0078-0.00310.00550.00020.26650.0182-0.03670.29810.01340.262421.82255.452476.3141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 6 through 482)A6 - 482
2X-RAY DIFFRACTION2(chain 'B' and resid 6 through 488)B6 - 488
3X-RAY DIFFRACTION3(chain 'B' and resid 509 through 510)B509 - 510
4X-RAY DIFFRACTION4(chain 'A' and resid 506 through 507)A506 - 507

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