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- PDB-5mby: Crystal Structure of Arg184Gln mutant of Human Prolidase with Mn ... -

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Basic information

Entry
Database: PDB / ID: 5mby
TitleCrystal Structure of Arg184Gln 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: 1.55 Å
AuthorsWilk, P. / Piwowarczyk, R. / 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_alt_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_alt_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.pdbx_ptnr2_label_alt_id / _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)108,90118
Polymers107,7142
Non-polymers1,18716
Water21,9601219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8120 Å2
ΔGint-54 kcal/mol
Surface area34930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.568, 107.091, 217.373
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
11B-687-

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: 53857.109 Da / Num. of mol.: 2 / Mutation: R184Q
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, 1235 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
#5: Chemical ChemComp-PRO / PROLINE / Proline


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1219 / 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: 2.8 Å3/Da / Density % sol: 56.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.9 / Details: 100mM NaCacodylate, 690-760mM NaCitrate

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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: Aug 25, 2016
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: 1.549→48.033 Å / Num. obs: 173821 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.74 % / Biso Wilson estimate: 18.33 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 11.37
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 6.58 % / Rmerge(I) obs: 1.375 / Mean I/σ(I) obs: 1.29 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.74 Å44.15 Å
Translation7.74 Å44.15 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PHASER2.5.7phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M4J

5m4j


Resolution: 1.55→48.03 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.34
RfactorNum. reflection% reflectionSelection details
Rfree0.174 2100 1.21 %Random selection
Rwork0.156 ---
obs0.156 173801 99.7 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.74 Å2
Refinement stepCycle: LAST / Resolution: 1.55→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7526 0 68 1219 8813
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017873
X-RAY DIFFRACTIONf_angle_d1.21910658
X-RAY DIFFRACTIONf_dihedral_angle_d13.6112902
X-RAY DIFFRACTIONf_chiral_restr0.0491157
X-RAY DIFFRACTIONf_plane_restr0.0071395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5492-1.58530.3361370.338511216X-RAY DIFFRACTION98
1.5853-1.62490.3121390.297311339X-RAY DIFFRACTION100
1.6249-1.66890.24421390.265311361X-RAY DIFFRACTION100
1.6689-1.7180.29241380.253411357X-RAY DIFFRACTION100
1.718-1.77340.2361400.242311431X-RAY DIFFRACTION100
1.7734-1.83680.25071390.220311321X-RAY DIFFRACTION100
1.8368-1.91030.20881400.190911471X-RAY DIFFRACTION100
1.9103-1.99730.16531390.168211377X-RAY DIFFRACTION100
1.9973-2.10260.16691400.151411410X-RAY DIFFRACTION100
2.1026-2.23430.16321400.140611454X-RAY DIFFRACTION100
2.2343-2.40680.18051400.135411474X-RAY DIFFRACTION100
2.4068-2.6490.16821400.134911492X-RAY DIFFRACTION100
2.649-3.03230.15381410.133611531X-RAY DIFFRACTION100
3.0323-3.82010.12741420.123211593X-RAY DIFFRACTION100
3.8201-48.05580.15031460.133711874X-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)
10.4189-0.174-0.08950.3113-0.25690.4442-0.0490.1560.1373-0.2554-0.0064-0.1463-0.060.020100.22870.0080.05520.21290.00750.213238.38432.29162.0806
20.46570.00920.01020.54790.00840.21020.0241-0.0074-0.05110.04080.0087-0.20790.00390.039800.16820.0034-0.01190.1794-00.216737.594326.004277.4296
30.3945-0.19310.08430.61030.13140.53210.03940.0885-0.2185-0.0276-0.0176-0.34180.04140.01650.00010.18350.00550.0290.2196-0.01450.270843.316417.632468.9864
40.3742-0.11620.16110.4563-0.32440.2365-0.0638-0.0712-0.00950.06180.0661-0.22370.01160.055900.15910.0121-0.01490.2168-0.0330.316848.300528.31278.5872
50.8283-0.3398-0.0290.97920.03310.0923-0.00760.03610.05-0.0620.0149-0.1753-0.0130.0087-0.00010.17820.0125-0.00080.18520.01310.160633.799635.532871.6116
60.12660.0488-0.0670.6958-0.15080.10960.0110.03850.0205-0.0623-0.00560.1686-0.0315-0.026400.17330.0128-0.02450.20490.00220.185710.639630.478872.2085
70.7038-0.0543-0.08721.14940.01320.24470.02080.06080.0471-0.0608-0.01330.2223-0.0443-0.0503-00.15920.0238-0.02940.17650.0130.17679.192942.268672.8507
81.1994-0.216-0.4511.21920.17730.50440.0025-0.11390.33480.05220.0449-0.1984-0.08130.05380.00010.17240.0131-0.01510.1622-0.01190.222720.339455.96978.391
90.1878-0.2483-0.11370.88040.08220.1205-0.0351-0.05350.12260.0990.0342-0.0286-0.07460.0258-00.20390.0233-0.00390.199-0.00620.20216.073254.30981.8048
100.21930.32970.13720.8743-0.07490.27480.07810.12760.2322-0.0883-0.01360.2023-0.0426-0.12240.02220.16280.02140.01140.17180.03550.225911.482150.790573.4748
110.2089-0.1341-0.0710.230.08020.09710.12750.41540.0777-0.412-0.11330.2837-0.0002-0.06110.16740.27840.0502-0.09230.28910.03710.22017.996644.200660.118
120.44920.3317-0.03840.37010.18470.43680.0232-0.0994-0.14690.28550.08140.3661-0.0525-0.219-0.3560.2720.01450.09580.21990.04380.22885.183215.014896.9572
130.1651-0.1425-0.03910.6187-0.17910.2689-0.03750.01950.04380.19660.0248-0.0174-0.06390.045500.24920.0044-0.00570.19740.01090.137919.677722.427995.8215
140.7693-0.16220.1950.38780.08450.5689-0.0584-0.03880.12740.35570.0550.1171-0.1931-0.1448-0.04030.35930.03180.05020.24640.01180.199210.536430.6261100.7407
150.30160.22950.19050.307-0.10050.5761-0.0251-0.12390.01410.37770.0854-0.1102-0.1140.08040.00150.42550.0189-0.02510.2489-0.00670.142321.493621.4958106.0246
160.2226-0.216-0.27130.8251-0.24680.7334-0.036-0.067-0.07090.24230.0230.09950.0302-0.1254-0.00040.22390.01660.01330.16410.01470.164814.397712.100992.966
170.3613-0.2129-0.0950.99760.17840.20980.02240.0752-0.0984-0.0811-0.01850.10110.0034-0.0495-00.16620.0026-0.02710.1922-0.02030.17116.08528.065569.0401
180.5466-0.1792-0.40860.7940.24870.9745-0.0374-0.0639-0.22180.2250.04840.00850.16670.0681-00.21070.0048-0.01760.17670.01150.232522.6932-8.016682.5128
190.34210.03990.10990.6288-0.30470.38240.07570.0473-0.1598-0.0235-0.0242-0.14520.0550.13050.00150.15840.0112-0.02170.2127-0.04560.266330.1558-8.79268.0877
200.5117-0.27850.06460.7533-0.0160.49180.01460.1335-0.1408-0.026-0.07350.2191-0.0004-0.1049-0.03330.1562-0.0099-0.02710.2158-0.02750.23788.47582.199970.7763
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 36 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 37 THROUGH 82 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 83 THROUGH 124 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 125 THROUGH 156 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 157 THROUGH 212 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 213 THROUGH 252 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 253 THROUGH 319 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 320 THROUGH 396 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 397 THROUGH 436 )
10X-RAY DIFFRACTION10CHAIN 'A' AND (RESID 437 THROUGH 464 )
11X-RAY DIFFRACTION11CHAIN 'A' AND (RESID 465 THROUGH 490 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 6 THROUGH 36 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 37 THROUGH 82 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 83 THROUGH 124 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 125 THROUGH 159 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 160 THROUGH 212 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 213 THROUGH 319 )
18X-RAY DIFFRACTION18CHAIN 'B' AND (RESID 320 THROUGH 407 )
19X-RAY DIFFRACTION19CHAIN 'B' AND (RESID 408 THROUGH 443 )
20X-RAY DIFFRACTION20CHAIN 'B' AND (RESID 444 THROUGH 489 )

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