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- PDB-5mbz: Crystal Structure of Ser202Phe mutant of Human Prolidase with Mn ... -

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Basic information

Entry
Database: PDB / ID: 5mbz
TitleCrystal Structure of Ser202Phe 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: 1.5 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.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 1.5Nov 13, 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)108,80219
Polymers107,7182
Non-polymers1,08417
Water20,2851126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-70 kcal/mol
Surface area36050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.785, 106.945, 216.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-730-

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: 53859.191 Da / Num. of mol.: 2 / Mutation: S202F
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, 1143 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 / Details: Substrate / 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 / Details: Substrate / Source: (synth.) Homo sapiens (human)
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / 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.: 1126 / 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: 55.71 %
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: Nov 14, 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: 1.499→47.934 Å / Num. obs: 191294 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.41 % / Biso Wilson estimate: 18.01 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 14.73
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 7.56 % / Rmerge(I) obs: 1.1 / Mean I/σ(I) obs: 1.87 / % possible all: 99.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation8.11 Å47.93 Å
Translation8.11 Å47.93 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
XSCALEdata scaling
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M4J

5m4j


Resolution: 1.5→46.79 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.18
RfactorNum. reflection% reflection
Rfree0.175 9565 5 %
Rwork0.15 --
obs0.151 191280 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 26.81 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7477 0 57 1126 8660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097922
X-RAY DIFFRACTIONf_angle_d1.2410747
X-RAY DIFFRACTIONf_dihedral_angle_d13.3582955
X-RAY DIFFRACTIONf_chiral_restr0.0741166
X-RAY DIFFRACTIONf_plane_restr0.0071409
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4992-1.51620.27743110.2775903X-RAY DIFFRACTION98
1.5162-1.53410.31053140.26925982X-RAY DIFFRACTION100
1.5341-1.55280.2983200.25836073X-RAY DIFFRACTION100
1.5528-1.57240.28373140.24275962X-RAY DIFFRACTION100
1.5724-1.59310.26173170.23786019X-RAY DIFFRACTION100
1.5931-1.6150.27453170.23476021X-RAY DIFFRACTION100
1.615-1.6380.24193150.22536000X-RAY DIFFRACTION100
1.638-1.66250.25793200.21786067X-RAY DIFFRACTION100
1.6625-1.68850.24063160.20586001X-RAY DIFFRACTION100
1.6885-1.71610.24253150.19976001X-RAY DIFFRACTION100
1.7161-1.74570.19733190.19156044X-RAY DIFFRACTION100
1.7457-1.77750.21453170.17856038X-RAY DIFFRACTION100
1.7775-1.81170.20833180.176034X-RAY DIFFRACTION100
1.8117-1.84870.20543170.1696026X-RAY DIFFRACTION100
1.8487-1.88890.21773170.16226027X-RAY DIFFRACTION100
1.8889-1.93280.18393180.15956041X-RAY DIFFRACTION100
1.9328-1.98110.17293180.15376030X-RAY DIFFRACTION100
1.9811-2.03470.16663190.14146076X-RAY DIFFRACTION100
2.0347-2.09460.17063170.13686014X-RAY DIFFRACTION100
2.0946-2.16220.16943200.13726082X-RAY DIFFRACTION100
2.1622-2.23950.1633180.13256036X-RAY DIFFRACTION100
2.2395-2.32910.15823210.12986112X-RAY DIFFRACTION100
2.3291-2.43510.13383180.12336042X-RAY DIFFRACTION100
2.4351-2.56350.16933210.13036090X-RAY DIFFRACTION100
2.5635-2.72410.15953200.1356081X-RAY DIFFRACTION100
2.7241-2.93440.17433200.13386082X-RAY DIFFRACTION100
2.9344-3.22960.1623240.1346156X-RAY DIFFRACTION100
3.2296-3.69680.14833220.12786124X-RAY DIFFRACTION100
3.6968-4.65690.14173270.12066198X-RAY DIFFRACTION100
4.6569-46.8090.17023350.16526353X-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)
10.4567-0.04480.03591.0508-0.24710.7436-0.0031-0.05620.03760.32030.0130.058-0.1008-0.0369-0.01170.24390.00880.0350.16640.00360.132114.517819.950494.1789
22.4747-0.9447-0.58631.0748-0.04640.20850.1452-0.43750.32450.23290.1227-0.3594-0.13590.2075-0.24170.3485-0.03920.0230.2769-0.05140.296122.522911.607666.8935
30.6534-0.2642-0.18621.36540.51160.9980.00080.025-0.10270.07880.0219-0.06510.0570.0556-0.02410.1106-0.01-0.00160.1325-0.00140.126821.8226-5.157375.6997
41.37450.4383-0.48231.3626-0.18131.8584-0.0620.20390.0671-0.0381-0.03120.2777-0.1335-0.28350.07860.13150.003-0.0160.1807-0.02620.18228.43323.025970.3112
50.90670.09760.04261.03510.13870.4289-0.00220.0185-0.0728-0.07120.0512-0.24510.01570.0507-0.04490.13380.00490.02390.1409-0.00170.16436.555328.576671.2599
60.02790.06220.1170.07550.02861.7608-0.2633-0.3865-0.10480.31970.165-0.18860.18210.47870.05370.31770.03020.01490.34650.08940.504212.036234.736178.5856
71.3201-0.3264-0.14441.32460.08210.4175-0.0251-0.12690.18420.01790.03680.1372-0.0878-0.0396-0.01550.14040.0229-0.00540.15020.00710.168715.943151.832876.4075
82.38320.266-0.12971.0972-0.27870.58070.09440.17980.2344-0.24390.00360.3058-0.0471-0.1303-0.09110.20290.0212-0.04890.16920.04440.24399.072948.012967.237
92.00022.00022.00012.000122-0.18710.3055-0.0536-0.12950.04530.0147-0.1266-0.03220.14180.1178-0.0141-0.02340.19030.03170.180322.55764.604578.3683
101.999922.00012.00011.99972.00020.17790.0486-0.1917-0.05040.1324-0.0344-0.1399-0.2799-0.3180.1859-0.02340.04680.21860.00980.235919.486543.233378.3671
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 8 THROUGH 236 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 237 THROUGH 273 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 274 THROUGH 445 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 446 THROUGH 491 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 8 THROUGH 236 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 237 THROUGH 266 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 267 THROUGH 438 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 439 THROUGH 490 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 1 THROUGH 2 )
10X-RAY DIFFRACTION10CHAIN 'D' AND (RESID 1 THROUGH 2 )

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