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- PDB-5mc4: Crystal Structure of Gly448Arg mutant of Human Prolidase with Mn ... -

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Basic information

Entry
Database: PDB / ID: 5mc4
TitleCrystal Structure of Gly448Arg 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 / 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 / : / HYDROXIDE ION / PROLINE / Xaa-Pro dipeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 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_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.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.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.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

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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)108,12814
Polymers107,3102
Non-polymers81812
Water11,602644
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6180 Å2
ΔGint-36 kcal/mol
Surface area35990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.742, 107.737, 210.878
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 53654.949 Da / Num. of mol.: 2 / Mutation: G448R
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 , 6 types, 656 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 / Hydroxide


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 644 / 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: 2.74 Å3/Da / Density % sol: 55.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 10mM NaBorate, 690-760mM NaCitrate / PH range: 7.6-8.2

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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: May 22, 2015
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: 1.799→47.971 Å / Num. obs: 109217 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.82 % / Biso Wilson estimate: 26.75 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 18.66
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 6.88 % / Rmerge(I) obs: 1.108 / Mean I/σ(I) obs: 1.71 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.71 Å48.04 Å
Translation7.71 Å48.04 Å

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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: 1.8→47.97 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.9
RfactorNum. reflection% reflection
Rfree0.192 2101 1.92 %
Rwork0.163 --
obs0.164 109215 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 36.28 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7333 0 42 644 8019
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077705
X-RAY DIFFRACTIONf_angle_d1.07410453
X-RAY DIFFRACTIONf_dihedral_angle_d13.6522886
X-RAY DIFFRACTIONf_chiral_restr0.041144
X-RAY DIFFRACTIONf_plane_restr0.0051370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.799-1.84080.33221370.29956977X-RAY DIFFRACTION98
1.8408-1.88690.30751390.27187087X-RAY DIFFRACTION100
1.8869-1.93790.30061380.25397050X-RAY DIFFRACTION100
1.9379-1.99490.24041400.23087126X-RAY DIFFRACTION100
1.9949-2.05930.21791390.20137076X-RAY DIFFRACTION100
2.0593-2.13290.23821390.18527125X-RAY DIFFRACTION100
2.1329-2.21830.20931390.17037091X-RAY DIFFRACTION100
2.2183-2.31930.18711400.16757126X-RAY DIFFRACTION100
2.3193-2.44150.20871400.15777107X-RAY DIFFRACTION100
2.4415-2.59450.19291400.15467148X-RAY DIFFRACTION100
2.5945-2.79480.1871400.15277152X-RAY DIFFRACTION100
2.7948-3.0760.16271400.15167165X-RAY DIFFRACTION100
3.076-3.5210.18171410.14177180X-RAY DIFFRACTION100
3.521-4.43560.15181420.13197254X-RAY DIFFRACTION100
4.4356-47.98760.19061470.16347450X-RAY DIFFRACTION100
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)
10.1248-0.0437-0.06520.4016-0.0390.023-0.0161-0.0540.02040.16290.00890.0705-0.0788-0.027100.3020.03220.02880.28370.06820.209312.914620.259793.9012
20.4604-0.1033-0.15730.7695-0.06320.44980.0282-0.1483-0.00590.22210.06450.0959-0.0972-0.06040.00030.31060.03410.03920.27040.03460.197614.088221.017196.5468
30.03530.04480.05570.1650.10470.07140.0234-0.095-0.0656-0.02620.0833-0.12180.0112-0.0222-00.27150.0301-0.02110.2434-0.00190.252915.847617.388765.3046
40.4949-0.06930.24580.66380.05930.75420.0605-0.0005-0.2291-0.01220.03450.10560.06060.055700.21420.0209-0.04930.23360.01660.247619.3929-2.914772.0906
50.86650.03970.22750.6591-0.01790.3464-0.0327-0.0029-0.0836-0.05840.027-0.14720.00650.033600.21520.03330.00720.22050.01220.226636.317630.281970.7153
60.01980.0308-0.00140.00910.0147-0.0174-0.1008-0.09740.08630.25370.0315-0.189-0.00640.046100.36750.0605-0.1070.4160.06250.44119.105334.125577.7012
70.9772-0.10760.16281.0405-0.09710.7577-0.1021-0.10640.17910.01670.08060.0697-0.1732-0.08-0.00160.21920.0748-0.02810.18910.00150.219114.696452.875173.5887
86.6263-2.56216.16431.9361-2.18955.7743-0.2406-0.1259-0.0830.23660.14390.1757-0.3355-0.24760.05940.34890.0663-0.07510.30830.0080.560122.38365.848776.2524
90.46691.03270.69213.86322.59771.75040.0146-0.00890.0125-0.03680.03190.00220.06620.0098-0.01820.54630.0959-0.08250.3185-0.03950.482718.896144.641277.8519
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 82 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 83 THROUGH 212 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 213 THROUGH 271 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 272 THROUGH 483 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 6 THROUGH 234 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 235 THROUGH 271 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 272 THROUGH 487 )
8X-RAY DIFFRACTION8CHAIN 'C' AND (RESID 1 THROUGH 2 )
9X-RAY DIFFRACTION9CHAIN 'D' AND (RESID 1 THROUGH 2 )

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