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- PDB-5m4l: Crystal Structure of Wild-Type Human Prolidase with Mg ions and L... -

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Basic information

Entry
Database: PDB / ID: 5m4l
TitleCrystal Structure of Wild-Type Human Prolidase with Mg ions and LeuPro ligand
ComponentsXaa-Pro dipeptidase
KeywordsHYDROLASE / prolidase / peptidase / hydrolysis / pita-bread / metalloenzyme / hydroxide ion
Function / homology
Function and homology information


Xaa-Pro dipeptidase / proline dipeptidase activity / negative regulation of programmed cell death / metallocarboxypeptidase activity / amino acid metabolic process / metalloaminopeptidase activity / collagen catabolic process / 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 ...: / 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
LEUCINE / HYDROXIDE ION / PROLINE / Xaa-Pro dipeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.49 Å
AuthorsWilk, P. / Weiss, M.S. / Mueller, U. / Dobbek, H.
CitationJournal: FEBS J. / Year: 2017
Title: Substrate specificity and reaction mechanism of human prolidase.
Authors: Wilk, P. / Uehlein, M. / Kalms, J. / Dobbek, H. / Mueller, U. / Weiss, M.S.
History
DepositionOct 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2017Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2017Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.4Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature / 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

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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)108,89020
Polymers107,5982
Non-polymers1,29118
Water20,7351151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7960 Å2
ΔGint-57 kcal/mol
Surface area35080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.605, 106.839, 216.990
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-677-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111CHAIN A AND SEGID
211CHAIN B AND SEGID

NCS ensembles :
ID
1
2

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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: 53799.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEPD, PRD / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P12955, Xaa-Pro dipeptidase

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Non-polymers , 7 types, 1169 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-OH / HYDROXIDE ION


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


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2 / 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 / Source: (synth.) Homo sapiens (human)
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1151 / 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: 55.73 %
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: 0.918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 3, 2015
RadiationMonochromator: Double Crystal Monochromator Si-11 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.49→47.925 Å / Num. obs: 193948 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.96 % / Biso Wilson estimate: 18.05 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 18.29
Reflection shellResolution: 1.49→1.58 Å / Rmerge(I) obs: 1.177 / Mean I/σ(I) obs: 1.6 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
XDSdata scaling
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementResolution: 1.49→46.75 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.24
RfactorNum. reflection% reflection
Rfree0.171 2101 1.08 %
Rwork0.146 --
obs0.146 193926 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 29.37 Å2
Refinement stepCycle: LAST / Resolution: 1.49→46.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7542 0 81 1151 8774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097976
X-RAY DIFFRACTIONf_angle_d1.22210812
X-RAY DIFFRACTIONf_dihedral_angle_d12.982962
X-RAY DIFFRACTIONf_chiral_restr0.051173
X-RAY DIFFRACTIONf_plane_restr0.0071417
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDType
11A5532X-RAY DIFFRACTIONPOSITIONAL
12B5532X-RAY DIFFRACTIONPOSITIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4921-1.52680.39371370.336412462X-RAY DIFFRACTION98
1.5268-1.5650.31111380.290712686X-RAY DIFFRACTION100
1.565-1.60730.26381400.26512711X-RAY DIFFRACTION100
1.6073-1.65460.26051390.23512758X-RAY DIFFRACTION100
1.6546-1.7080.25531390.213312668X-RAY DIFFRACTION100
1.708-1.76910.23781400.196412766X-RAY DIFFRACTION100
1.7691-1.83990.19341390.182512734X-RAY DIFFRACTION100
1.8399-1.92370.21191400.163512739X-RAY DIFFRACTION100
1.9237-2.02510.18661400.14412785X-RAY DIFFRACTION100
2.0251-2.1520.16771400.132912778X-RAY DIFFRACTION100
2.152-2.31810.15781400.124912818X-RAY DIFFRACTION100
2.3181-2.55140.17451410.125812842X-RAY DIFFRACTION100
2.5514-2.92050.13041400.126612855X-RAY DIFFRACTION100
2.9205-3.67930.16481420.118612965X-RAY DIFFRACTION100
3.6793-46.77020.12521460.126113258X-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)
10.1649-0.1009-0.01170.68560.15630.3540.01740.0217-0.0351-0.07450.0316-0.3112-0.00310.02890.00820.1564-0.00670.02380.1771-0.00160.229639.900827.771970.9825
20.7473-0.30420.0320.97860.11660.2484-0.00380.0278-0.0349-0.06760.0594-0.27660.01180.03410.00260.1470.00130.0060.1738-0.00360.218639.029828.734772.4001
30.6039-0.24-0.08021.08050.12220.1735-0.01120.00060.1342-0.03960.01650.0806-0.0354-0.0272-00.16320.0173-0.01760.17690.01540.185515.41346.096974.9506
40.10650.12720.05980.4465-0.14710.1515-0.0991-0.08540.08360.16660.02470.2357-0.0043-0.0224-00.21840.03980.03780.2229-0.01870.28167.569455.642684.6254
50.206-0.0036-0.00290.47030.05510.07520.09810.16120.1476-0.2333-0.07210.1778-0.0794-0.05750.01270.21730.0329-0.0470.22960.04480.207411.962845.842863.6979
60.5148-0.21030.06710.80430.03110.3918-0.0444-0.04660.05180.38920.06910.1078-0.0755-0.04950.03180.30490.02370.04140.18240.01650.113414.087223.16199.7335
70.3888-0.0605-0.05820.02220.03670.4361-0.0701-0.1152-0.07170.4110.0586-0.0508-0.0970.0256-0.1850.42970.0231-0.0530.21930.02550.122122.847114.6302103.9361
80.0982-0.18960.04470.7580.1520.11990.02870.0525-0.0945-0.0499-0.02280.1136-0.005-0.058-00.1601-0.0052-0.01880.1914-0.0130.176614.00518.391670.576
90.37-0.09610.02760.4314-0.07860.3898-0.0323-0.0178-0.1880.240.060.01460.18170.0520.05330.1557-0.0001-0.01140.11160.00760.141122.6018-7.892782.3436
100.12940.12940.05370.3726-0.16880.1990.0547-0.0197-0.18490.0327-0.0084-0.1553-00.10140.01310.13780.0097-0.01260.2119-0.0410.253130.2125-8.809367.8808
110.2857-0.1026-0.06830.44560.06590.1547-0.03220.1459-0.2035-0.011-0.08560.2480.0665-0.121-0.06380.1516-0.0129-0.02590.2225-0.01960.22918.28952.791470.5337
120.00050.00610.00150.30040.080.0222-0.0517-0.0052-0.01730.0088-0.02690.00510.04080.009-0.00030.29090.0267-0.03660.5652-0.06980.535719.258542.064978.6053
130.033-0.1039-0.00260.34220.0080.00210.05560.030.038-0.01280.0520.01530.01740.00440.00040.41250.0296-0.12710.5952-0.10410.534322.33045.295478.722
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 101 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 102 THROUGH 212 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 213 THROUGH 407 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 408 THROUGH 443 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 444 THROUGH 489 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 6 THROUGH 155 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 156 THROUGH 188 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 189 THROUGH 319 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 320 THROUGH 407 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 408 THROUGH 443 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 444 THROUGH 489 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 1 THROUGH 2 )
13X-RAY DIFFRACTION13CHAIN 'D' AND (RESID 1 THROUGH 2 )

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