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- PDB-6h2p: Crystal Structure of Arg184Gln mutant of Human Prolidase with Mn ... -

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Basic information

Entry
Database: PDB / ID: 6h2p
TitleCrystal Structure of Arg184Gln mutant of Human Prolidase with Mn ions and Cacodylate 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
CACODYLATE ION / : / Xaa-Pro dipeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.479 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 29, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Apr 22, 2020Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.3Jan 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 / 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
Revision 1.4Oct 23, 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)109,98413
Polymers109,0302
Non-polymers95411
Water23,5821309
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8510 Å2
ΔGint-54 kcal/mol
Surface area34510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.453, 107.075, 216.543
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
11A-692-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA6 - 500
211chain BB6 - 500

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Components

#1: Protein Xaa-Pro dipeptidase / X-Pro dipeptidase / Imidodipeptidase / Peptidase D / Proline dipeptidase / Prolidase


Mass: 54514.898 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
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6AsO2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1309 / Source method: isolated from a natural source / Formula: H2O
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: 55.22 %
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, 1.8932
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 wavelength
IDWavelength (Å)Relative weight
10.91841
21.89321
ReflectionResolution: 1.479→47.991 Å / Num. obs: 198755 / % possible obs: 99.8 % / Redundancy: 5.674 % / Biso Wilson estimate: 23 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.0502 / Rrim(I) all: 0.127 / Net I/σ(I): 10.76
Reflection shellResolution: 1.479→1.57 Å / Redundancy: 6.4 % / Mean I/σ(I) obs: 1.25 / Num. unique obs: 31784 / CC1/2: 0.522 / Rpim(I) all: 0.593 / Rrim(I) all: 1.509 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5MBY

5mby


Resolution: 1.479→47.991 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.82
RfactorNum. reflection% reflection
Rfree0.1704 2101 1.06 %
Rwork0.148 --
obs0.1482 198703 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 142.19 Å2 / Biso mean: 26.9542 Å2 / Biso min: 11.89 Å2
Refinement stepCycle: final / Resolution: 1.479→47.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7460 0 96 1309 8865
Biso mean--48.36 36.53 -
Num. residues----959
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0158020
X-RAY DIFFRACTIONf_angle_d1.61110864
X-RAY DIFFRACTIONf_chiral_restr0.0821185
X-RAY DIFFRACTIONf_plane_restr0.0091419
X-RAY DIFFRACTIONf_dihedral_angle_d13.862972
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5306X-RAY DIFFRACTION7.463TORSIONAL
12B5306X-RAY DIFFRACTION7.463TORSIONAL
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 (%)
1.479-1.51340.39471370.3324127961293398
1.5134-1.55130.31341390.30261307513214100
1.5513-1.59320.30941390.26151298913128100
1.5932-1.64010.23941390.23461299813137100
1.6401-1.6930.20331400.21341310613246100
1.693-1.75360.23481390.20111300813147100
1.7536-1.82380.19481400.17961305513195100
1.8238-1.90680.19731400.16031311013250100
1.9068-2.00730.1641390.14131307813217100
2.0073-2.13310.1611400.1311310113241100
2.1331-2.29780.1731400.12321307913219100
2.2978-2.5290.1281410.12481314913290100
2.529-2.89490.15351410.13071322313364100
2.8949-3.64710.15111410.12311324213383100
3.6471-48.01630.141460.12631359313739100
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)
10.4113-0.10430.05460.7298-0.03820.2966-0.0129-0.0565-0.01120.27980.03410.0689-0.0223-0.0228-0.02220.24210.00710.02220.18550.01910.1513.631819.363596.0048
20.5177-0.07190.2510.94050.17480.8202-0.0491-0.09590.01830.33230.04840.061-0.0837-0.02270.00380.27180.00940.02990.17870.01240.138414.676720.44598.1519
30.3676-0.2079-0.07880.84150.16660.20630.03030.1028-0.0864-0.0891-0.03380.05360.0078-0.0589-0.00190.15130.0026-0.01680.1803-0.01780.154516.33178.059268.7348
40.7275-0.2893-0.21011.09740.33910.8582-0.01130.0208-0.16830.10240.00650.01810.09720.0289-0.00980.146-0.0065-0.01210.1425-0.00450.191221.2216-6.423976.4669
50.74320.0997-0.00670.87170.01410.40610.02890.06280.0204-0.0534-0.0016-0.2177-0.02740.0354-0.02750.15240.00770.01950.1627-0.00070.191137.786728.503970.9241
60.65870.28550.16531.9606-0.25120.92780.06270.0965-0.1339-0.11410.0362-0.25430.05130.0101-0.08250.14030.01220.00990.1764-0.02070.245441.868314.92169.5422
70.4387-0.33470.30581.0329-0.18960.2194-0.0691-0.0526-0.00020.03850.0747-0.28090.01720.061-0.00130.15820.0113-0.01010.1972-0.01830.314947.79728.648578.7297
80.7582-0.1761-0.13210.99510.02070.1649-0.00210.05140.1229-0.0625-0.0061-0.1685-0.01150.01840.00160.15760.01350.01460.16070.00720.150733.767235.616670.6594
90.8844-0.4946-0.17991.23560.04160.332-0.02190.03240.01320.0021-0.00370.1463-0.0373-0.03620.0220.14520.0084-0.01320.16290.00720.1648.638233.088774.9542
100.7089-0.2729-0.14631.110.16390.290.04640.09160.0922-0.1309-0.05510.1561-0.0683-0.05020.00610.16930.0226-0.02230.17080.02290.175611.200545.597768.5541
111.2419-0.5801-0.38951.24750.17680.3304-0.0257-0.09320.2840.08750.0493-0.1344-0.05110.0222-0.02750.16070.0142-0.0150.1487-0.01060.202318.692755.460279.294
121.85420.0708-0.39311.1231-0.15070.93310.06220.04490.2327-0.0429-0.03090.1315-0.0611-0.0717-0.06650.15210.0088-0.00970.14690.02740.200711.444150.915973.1727
136.3684-1.0378-0.01320.389-0.10550.38060.03130.81190.0303-0.3254-0.09420.23420.012-0.04340.03470.25890.0337-0.07040.28830.01730.19677.359943.713259.6749
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 82 )A6 - 82
2X-RAY DIFFRACTION2chain 'A' and (resid 83 through 211 )A83 - 211
3X-RAY DIFFRACTION3chain 'A' and (resid 212 through 319 )A212 - 319
4X-RAY DIFFRACTION4chain 'A' and (resid 320 through 482 )A320 - 482
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 82 )B6 - 82
6X-RAY DIFFRACTION6chain 'B' and (resid 83 through 124 )B83 - 124
7X-RAY DIFFRACTION7chain 'B' and (resid 125 through 159 )B125 - 159
8X-RAY DIFFRACTION8chain 'B' and (resid 160 through 212 )B160 - 212
9X-RAY DIFFRACTION9chain 'B' and (resid 213 through 277 )B213 - 277
10X-RAY DIFFRACTION10chain 'B' and (resid 278 through 319 )B278 - 319
11X-RAY DIFFRACTION11chain 'B' and (resid 320 through 436 )B320 - 436
12X-RAY DIFFRACTION12chain 'B' and (resid 437 through 464 )B437 - 464
13X-RAY DIFFRACTION13chain 'B' and (resid 465 through 489 )B465 - 489

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