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- PDB-2okn: Crystal Strcture of Human Prolidase -

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Basic information

Entry
Database: PDB / ID: 2okn
TitleCrystal Strcture of Human Prolidase
ComponentsXaa-Pro dipeptidase
KeywordsHYDROLASE / METALLOCARBOXYPEPTIDASE / DISEASE MUTATION / XAA-PRO DIPEPTIDASE / DIPEPTIDASE / PEPTIDASE D / COLLAGEN DEGRADATION / METALLOAMINOPEPTIDASE / ENZYME / PROTEASE / PEPD GENE / MANGANESE / METAL-BINDING / METALLOPROTEASE / PHOSPHORYLATION / Structural Genomics / Protein Structure Factory / PSF
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 / 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
: / HYDROGENPHOSPHATE ION / Xaa-Pro dipeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsMueller, U. / Niesen, F.H. / Roske, Y. / Goetz, F. / Behlke, J. / Buessow, K. / Heinemann, U. / Protein Structure Factory (PSF)
CitationJournal: To be Published
Title: Crystal Structure of Human Prolidase: The Molecular Basis of PD Disease.
Authors: MUELLER, U. / NIESEN, F.H. / ROSKE, Y. / GOETZ, F. / BEHLKE, J. / BUESSOW, K. / HEINEMANN, U.
History
DepositionJan 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)109,8329
Polymers109,3242
Non-polymers5087
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-47 kcal/mol
Surface area35690 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)103.890, 108.960, 212.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is a homodimer located within the asymmetric unit

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Components

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


Mass: 54661.992 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEPD, PRD / Plasmid: RZPD CLONE ID PSFEP250H122 / Production host: Escherichia coli (E. coli) / Strain (production host): SCS1/PRARE / 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-PI / HYDROGENPHOSPHATE ION


Mass: 95.979 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: HO4P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.74 Å3/Da / Density % sol: 55.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.5M sodium/potassium phosphate, 0.05M sodium chloride, 0.02% sodium acide, 0.02M dithiothreitol, 0.02M manganese chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91838
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 28, 2004
RadiationMonochromator: Si 111 double-crystal-monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91838 Å / Relative weight: 1
ReflectionResolution: 2.45→37.53 Å / Num. all: 44429 / Num. obs: 44429 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.14 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.041 / Rsym value: 0.041 / Net I/σ(I): 26.2
Reflection shellResolution: 2.45→2.5 Å / Redundancy: 4.16 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 9.7 / Num. unique all: 2626 / Rsym value: 0.14 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345CCDdata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2iw2

2iw2


Resolution: 2.45→36.94 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.906 / SU B: 14.813 / SU ML: 0.179 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.378 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2221 5 %RANDOM
Rwork0.178 ---
all0.18 44426 --
obs0.18 44426 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 41.144 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20 Å20 Å2
2---2.42 Å20 Å2
3---1.5 Å2
Refinement stepCycle: LAST / Resolution: 2.45→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7432 0 19 301 7752
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0217728
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.94810477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1365977
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43123.115366
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.054151284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6341562
X-RAY DIFFRACTIONr_chiral_restr0.0950.21132
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025956
X-RAY DIFFRACTIONr_nbd_refined0.2050.23480
X-RAY DIFFRACTIONr_nbtor_refined0.3030.25197
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2396
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3210.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.210
X-RAY DIFFRACTIONr_mcbond_it1.03624926
X-RAY DIFFRACTIONr_mcangle_it1.63537670
X-RAY DIFFRACTIONr_scbond_it1.05823197
X-RAY DIFFRACTIONr_scangle_it1.56432796
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 165 -
Rwork0.206 3123 -
obs-3288 100 %
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)
10.3967-0.1122-0.13330.68140.58541.80430.0668-0.1192-0.02770.1549-0.0345-0.14920.03650.149-0.0323-0.09780.0251-0.02690.1265-0.004-0.18291.69833.99496.169
22.4567-0.1781-0.59351.5591-0.22621.72490.0134-0.1035-0.32980.21830.0224-0.05160.39240.0939-0.0358-0.01340.0176-0.060.091-0.0477-0.19888.73132.465100.018
30.7339-0.080.54352.0401-0.57232.54980.0120.04030.1201-0.06350.0586-0.1133-0.04940.0105-0.0706-0.12290.03270.0570.0716-0.0075-0.177690.28439.56867.852
40.55880.0580.07581.1169-0.16281.03970.03070.02250.1364-0.03230.0306-0.0526-0.108-0.0186-0.0613-0.14440.04050.05190.10870.0023-0.153784.32857.09371.948
51.46760.4455-0.11231.21070.17740.36540.0189-0.0010.0673-0.04810.02020.19350.0234-0.0715-0.039-0.12710.04610.00110.11680.0024-0.165264.13224.9670.392
61.8655-0.501-0.19361.4603-0.57840.897-0.0355-0.03610.15460.01930.07250.1708-0.1665-0.0044-0.037-0.1230.0041-0.01540.131-0.004-0.115560.44726.20173.81
70.8856-0.28670.17381.5427-0.22540.0538-0.0558-0.0795-0.0579-0.08650.031-0.16990.00720.08660.0249-0.13630.05350.05010.1298-0.0135-0.14493.42720.6170.638
81.7323-0.48090.37591.6017-0.00410.71730.0263-0.0675-0.22740.00490.027-0.13250.16190.0074-0.0533-0.11150.03870.0260.0742-0.0088-0.171689.5451.83474.513
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA7 - 1007 - 100
22AA101 - 197101 - 197
33AA198 - 258198 - 258
44AA259 - 483259 - 483
55BB7 - 1007 - 100
66BB101 - 197101 - 197
77BB198 - 267198 - 267
88BB268 - 483268 - 483

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