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- PDB-6h2q: Crystal Structure of Arg184Gln mutant of Human Prolidase with Mn ... -

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Basic information

Entry
Database: PDB / ID: 6h2q
TitleCrystal Structure of Arg184Gln mutant of Human Prolidase with Mn ions and LeuPro 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
LEUCINE / : / PROLINE / Xaa-Pro dipeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.78 Å
AuthorsWilk, P. / Piwowarczyk, R. / 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
DepositionJul 14, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 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 1.2Apr 22, 2020Group: Data collection / Database references
Category: diffrn_radiation_wavelength / diffrn_source / pdbx_related_exp_data_set
Item: _diffrn_source.pdbx_wavelength_list
Revision 1.3Oct 16, 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 / 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)110,16113
Polymers109,1722
Non-polymers98911
Water19,2761070
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6730 Å2
ΔGint-36 kcal/mol
Surface area35000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.559, 106.661, 217.432
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
11B-732-

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: 54585.980 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(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: P12955, Xaa-Pro dipeptidase

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Non-polymers , 5 types, 1081 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO2
#5: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1070 / 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: 2.75 Å3/Da / Density % sol: 55.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / 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: 1.78→47.88 Å / Num. obs: 776794 / % possible obs: 99.8 % / Redundancy: 6.77 % / Biso Wilson estimate: 28.26 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.0454 / Rrim(I) all: 0.118 / Net I/σ(I): 13.58
Reflection shellResolution: 1.78→1.89 Å / Redundancy: 6.82 % / Mean I/σ(I) obs: 1.77 / Num. unique obs: 18252 / CC1/2: 0.72 / Rpim(I) all: 0.421 / Rrim(I) all: 1.1 / % possible all: 99.3

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementResolution: 1.78→46.748 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.65
RfactorNum. reflection% reflection
Rfree0.1794 2099 1.83 %
Rwork0.1531 --
obs0.1536 114771 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 163.69 Å2 / Biso mean: 32.2598 Å2 / Biso min: 15.93 Å2
Refinement stepCycle: final / Resolution: 1.78→46.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7455 0 120 1071 8646
Biso mean--54.77 38.23 -
Num. residues----958
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067838
X-RAY DIFFRACTIONf_angle_d0.91510631
X-RAY DIFFRACTIONf_chiral_restr0.0351157
X-RAY DIFFRACTIONf_plane_restr0.0041396
X-RAY DIFFRACTIONf_dihedral_angle_d13.0882910
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 (%)
1.7799-1.82130.32261360.2927326746298
1.8213-1.86690.31731390.270774467585100
1.8669-1.91730.28191390.248374537592100
1.9173-1.97380.27251390.216474417580100
1.9738-2.03750.22681380.274447582100
2.0375-2.11030.21271390.174275137652100
2.1103-2.19480.17641400.16174817621100
2.1948-2.29470.19461390.149774587597100
2.2947-2.41560.19451400.150675327672100
2.4156-2.5670.15191400.150874967636100
2.567-2.76520.16781400.147775097649100
2.7652-3.04340.16111400.139375587698100
3.0434-3.48360.16791410.129375557696100
3.4836-4.38850.1311430.115176437786100
4.3885-46.76410.16911460.145478177963100
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)
10.797-0.1495-0.01030.82940.02970.7286-0.00990.0703-0.0964-0.09650.0316-0.27950.05330.00910.00060.2414-0.0070.01260.2435-0.00460.280239.589924.45470.5295
20.1804-0.02780.22370.2839-0.33350.4226-0.089-0.0620.0240.08510.0851-0.29640.02030.1385-00.23420.0152-0.02570.3016-0.04070.418848.768327.886778.3538
30.35380.055-0.11390.3520.24630.2539-0.0468-0.18280.05910.09510.111-0.35970.0409-0.02420.00010.27680.011-0.05750.3012-0.00210.445.381834.961779.9172
40.4993-0.06870.05791.2318-0.13590.303-0.01650.04080.0351-0.07350.02550.2094-0.0118-0.067300.23860.0112-0.04010.26260.00870.226611.983334.477570.887
50.8892-0.0702-0.24841.33970.01150.5284-0.0265-0.07860.32680.04030.0305-0.0446-0.1526-0.004800.2960.027-0.01730.26190.00640.314318.160555.629976.5304
60.1621-0.01230.33571.363-0.10270.64390.0029-0.16130.19590.21810.0130.1432-0.1715-0.14020.00010.31490.03690.00580.2944-0.00820.305611.986253.564481.6515
70.2675-0.3918-0.00730.53970.11590.3297-0.03050.56510.1713-0.37710.01890.1996-0.053-0.1110.03960.36650.0271-0.06170.35440.05070.284913.611545.537561.1936
80.7659-0.16570.14740.9287-0.05650.4645-0.0558-0.1140.03710.3970.08190.1712-0.1348-0.0987-0.00130.38940.03450.04520.31530.02880.239412.896623.58897.7203
90.21580.11710.18820.2548-0.03950.1949-0.0608-0.2560.09490.42960.1446-0.1392-0.12160.10980.09680.57860.0478-0.01920.4172-0.01860.259821.622721.4816106.0883
100.4598-0.1948-0.24760.1854-0.10510.431-0.0667-0.1816-0.01270.48260.1072-0.0861-0.01720.0765-0.08270.54710.0432-0.04170.37240.03250.266622.302714.4833105.1619
110.6271-0.30070.01851.35470.13080.22740.01230.05-0.179-0.0589-0.00380.14380.0165-0.042500.2331-0.015-0.03150.2589-0.01130.27114.88474.696872.5116
120.4492-0.098-0.08280.6348-0.19730.5372-0.0472-0.0879-0.2480.22310.09190.0330.14120.1125-0.00010.3022-0.0008-0.02070.2750.01990.317323.4989-5.357783.1829
130.4779-0.00230.39681.0186-0.10610.31740.07180.1796-0.2588-0.0944-0.0378-0.16740.07150.10940.00020.25380.003-0.01690.3009-0.03510.342528.6679-7.500967.8309
140.242-0.2181-0.04830.50950.19810.23420.04170.0771-0.2048-0.04-0.00760.43120.0803-0.284-0.0290.2586-0.025-0.04260.3314-0.03110.44334.74020.233471.4751
155.5050.69036.0159.3021-3.36888.430.04810.0593-0.05610.2401-0.05550.07-0.01620.1033-0.07090.42870.11430.04450.35810.03260.512819.771639.802977.8012
161.40512.35771.98486.57275.60074.78220.0053-0.2461-0.0103-0.12470.0272-0.29280.066-0.10340.09910.2576-0.0152-0.0830.41440.00410.402921.22577.137579.1966
174.46596.5180.43219.55970.72064.0806-0.0143-0.0779-0.11010.19310.36210.2226-0.5299-0.5614-0.42010.46030.0643-0.09060.4153-0.03610.450523.2372.819979.0744
182.03261.9771-1.94142.0161-1.77132.0015-0.39440.5862-0.6562-0.22720.3464-0.3152-0.06180.1062-0.00470.33360.0975-0.03140.5833-0.11750.464619.341744.4979.3761
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 124 )A6 - 124
2X-RAY DIFFRACTION2chain 'A' and (resid 125 through 155 )A125 - 155
3X-RAY DIFFRACTION3chain 'A' and (resid 156 through 188 )A156 - 188
4X-RAY DIFFRACTION4chain 'A' and (resid 189 through 299 )A189 - 299
5X-RAY DIFFRACTION5chain 'A' and (resid 300 through 396 )A300 - 396
6X-RAY DIFFRACTION6chain 'A' and (resid 397 through 452 )A397 - 452
7X-RAY DIFFRACTION7chain 'A' and (resid 453 through 487 )A453 - 487
8X-RAY DIFFRACTION8chain 'B' and (resid 6 through 124 )B6 - 124
9X-RAY DIFFRACTION9chain 'B' and (resid 125 through 159 )B125 - 159
10X-RAY DIFFRACTION10chain 'B' and (resid 160 through 188 )B160 - 188
11X-RAY DIFFRACTION11chain 'B' and (resid 189 through 343 )B189 - 343
12X-RAY DIFFRACTION12chain 'B' and (resid 344 through 416 )B344 - 416
13X-RAY DIFFRACTION13chain 'B' and (resid 417 through 457 )B417 - 457
14X-RAY DIFFRACTION14chain 'B' and (resid 458 through 483 )B458 - 483
15X-RAY DIFFRACTION15chain 'A' and (resid 506 through 506 )A506
16X-RAY DIFFRACTION16chain 'B' and (resid 503 through 503 )B503
17X-RAY DIFFRACTION17chain 'B' and (resid 504 through 504)B504
18X-RAY DIFFRACTION18chain 'A' and (resid 507 through 507 )A507

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