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- PDB-6srf: Crystal Structure of Human Prolidase G278N variant expressed in t... -

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Basic information

Entry
Database: PDB / ID: 6srf
TitleCrystal Structure of Human Prolidase G278N variant expressed in the presence of chaperones
ComponentsXaa-Pro dipeptidase
KeywordsHYDROLASE / dipeptidase / metallohydrolase / prolidase / pathological variants
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 / : / PROLINE / Xaa-Pro dipeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.847 Å
AuthorsWator, E. / Wilk, P.
CitationJournal: Febs Lett. / Year: 2020
Title: Co-expression with chaperones can affect protein 3D structure as exemplified by loss-of-function variants of human prolidase.
Authors: Wator, E. / Rutkiewicz, M. / Weiss, M.S. / Wilk, P.
History
DepositionSep 5, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _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 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)109,08311
Polymers108,4552
Non-polymers6289
Water18,6281034
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-38 kcal/mol
Surface area35070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.557, 106.692, 216.699
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-921-

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: 54227.551 Da / Num. of mol.: 2 / Mutation: G278D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PEPD, PRD / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Variant (production host): Arctic Express / References: UniProt: P12955, Xaa-Pro dipeptidase

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Non-polymers , 6 types, 1043 molecules

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


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Chemical ChemComp-PRO / PROLINE / Proline


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


Mass: 18.015 Da / Num. of mol.: 1034 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 10mM NaBorate, 690-760mM NaCitrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.847→47.86 Å / Num. obs: 102309 / % possible obs: 99.5 % / Redundancy: 7.33 % / Biso Wilson estimate: 30.5 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.171 / Net I/av σ(I): 10.8 / Net I/σ(I): 10.8
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 1.02 % / Rmerge(I) obs: 1.622 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 16073 / CC1/2: 0.479 / % possible all: 97.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5m4g

5m4g


Resolution: 1.847→47.86 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.92
RfactorNum. reflection% reflection
Rfree0.2165 2101 2.05 %
Rwork0.1802 --
obs0.181 102287 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 182.65 Å2 / Biso mean: 38.5343 Å2 / Biso min: 14.08 Å2
Refinement stepCycle: final / Resolution: 1.847→47.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7519 0 66 1034 8619
Biso mean--37.75 42.65 -
Num. residues----961
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.847-1.88950.3281310.3323623694
1.8895-1.93680.38041390.32076629100
1.9368-1.98910.30321400.30196659100
1.9891-2.04770.33331390.26746655100
2.0477-2.11380.24891390.22896643100
2.1138-2.18930.26371410.20996693100
2.1893-2.2770.24681390.20026642100
2.277-2.38060.2521400.19616679100
2.3806-2.50610.23531390.18686659100
2.5061-2.66310.23391410.18576728100
2.6631-2.86870.24471410.17156706100
2.8687-3.15730.18721400.16266698100
3.1573-3.61410.16571420.14256744100
3.6141-4.55280.16141430.13196810100
4.5528-47.860.20481470.17247005100
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)
10.4386-0.0832-0.14541.10450.05950.5322-0.006-0.0595-0.03760.45110.0282-0.09140.0380.0195-0.01760.35610.0039-0.04550.2278-0.00790.1672-14.6805-20.1592-10.71
21.4175-0.70671.18551.6606-0.76371.6247-0.0821-0.14620.08290.05030.05250.0277-0.1523-0.24830.00260.1839-0.00150.01040.233-0.00150.2109-15.3252-15.4321-39.2709
30.6268-0.20380.09961.5105-0.4860.82980.01140.0330.07670.09960.00550.1331-0.0252-0.0224-0.01840.1838-0.01150.00960.22050.0050.2077-21.89913.5466-33.8153
41.2645-0.12820.2511.71741.0124.39030.02170.12470.08680.0440.0528-0.4865-0.11410.4443-0.07510.1841-0.0255-0.0090.23780.03290.3238-5.25440.6703-35.7299
53.8998-0.05721.19535.4371.04411.6434-0.03210.2266-0.0495-0.331-0.08-0.03420.21970.17270.11970.26220.01460.02110.340.04230.3024-22.4254-4.5503-29.7073
60.79820.0866-0.15851.3794-0.27680.4997-0.01880.0330.0501-0.10820.10420.4056-0.0129-0.0957-0.08840.19820.002-0.03850.21740.01420.2658-39.5542-28.4471-36.67
71.9105-0.52611.2371.7012-0.62571.8359-0.0447-0.1983-0.35770.08780.1203-0.02960.037-0.1794-0.06030.2012-0.00570.03560.2301-0.00150.2463-10.7322-30.6684-36.2805
80.85510.20170.30850.5904-0.26640.31760.0003-0.07570.0018-0.0281-0.0191-0.3764-0.0020.0530.02350.21850.01880.03550.2439-0.01970.3175-9.4277-42.2302-35.5767
90.9046-0.11870.0841.8182-0.20940.6197-0.031-0.1087-0.27870.06240.0373-0.11580.10480.0213-0.00430.19210.0186-0.0070.20270.00770.2334-17.0171-55.1269-28.7961
103.1840.52320.16031.2646-0.32731.02880.02440.4625-0.2327-0.52070.0074-0.28690.06320.0891-0.02770.33270.03540.06730.2773-0.04910.24-14.7396-46.1806-46.7428
111.6848-0.31140.27018.7117-7.38546.26150.02990.17650.2351-0.1046-0.0609-0.0574-0.20360.0850.01720.2940.04830.01120.3736-0.02010.3016-19.3666-43.1293-29.9928
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 212 )A6 - 212
2X-RAY DIFFRACTION2chain 'A' and (resid 213 through 252 )A213 - 252
3X-RAY DIFFRACTION3chain 'A' and (resid 253 through 457 )A253 - 457
4X-RAY DIFFRACTION4chain 'A' and (resid 458 through 480 )A458 - 480
5X-RAY DIFFRACTION5chain 'A' and (resid 504 through 505 )A504 - 505
6X-RAY DIFFRACTION6chain 'B' and (resid 6 through 212 )B6 - 212
7X-RAY DIFFRACTION7chain 'B' and (resid 213 through 252 )B213 - 252
8X-RAY DIFFRACTION8chain 'B' and (resid 253 through 319 )B253 - 319
9X-RAY DIFFRACTION9chain 'B' and (resid 320 through 452 )B320 - 452
10X-RAY DIFFRACTION10chain 'B' and (resid 453 through 480 )B453 - 480
11X-RAY DIFFRACTION11chain 'B' and (resid 503 through 504 )B - D503 - 504

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