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- PDB-5x49: Crystal Structure of Human mitochondrial X-prolyl Aminopeptidase ... -

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Basic information

Entry
Database: PDB / ID: 5x49
TitleCrystal Structure of Human mitochondrial X-prolyl Aminopeptidase (XPNPEP3)
ComponentsProbable Xaa-Pro aminopeptidase 3
KeywordsHYDROLASE / XPNPEP3 / X-prolyl aminopeptidase / M24B / Icp55 / Human
Function / homology
Function and homology information


Xaa-Pro aminopeptidase / glomerular filtration / metalloaminopeptidase activity / aminopeptidase activity / protein processing / manganese ion binding / protein homodimerization activity / mitochondrion / proteolysis / cytosol / cytoplasm
Similarity search - Function
Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like
Similarity search - Domain/homology
(2S,3R)-3-amino-2-hydroxy-4-phenylbutanoic acid / : / Xaa-Pro aminopeptidase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSingh, R. / Kumar, A. / Ghosh, B. / Jamdar, S. / Makde, R.D.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structure of the human aminopeptidase XPNPEP3 and comparison of its in vitro activity with Icp55 orthologs: Insights into diverse cellular processes.
Authors: Singh, R. / Jamdar, S.N. / Goyal, V.D. / Kumar, A. / Ghosh, B. / Makde, R.D.
History
DepositionFeb 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _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 2.1Nov 22, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable Xaa-Pro aminopeptidase 3
B: Probable Xaa-Pro aminopeptidase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,90118
Polymers102,6052
Non-polymers2,29616
Water16,538918
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7150 Å2
ΔGint-13 kcal/mol
Surface area35400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.897, 135.103, 67.205
Angle α, β, γ (deg.)90.00, 99.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable Xaa-Pro aminopeptidase 3 / X-Pro aminopeptidase 3 / Aminopeptidase P3 / APP3


Mass: 51302.508 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 54-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: XPNPEP3 / Plasmid: pST50Str / Details (production host): pET3a based / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9NQH7, Xaa-Pro aminopeptidase

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Non-polymers , 6 types, 934 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-12P / DODECAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 546.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H50O13 / Comment: precipitant*YM
#4: Chemical ChemComp-01B / (2S,3R)-3-amino-2-hydroxy-4-phenylbutanoic acid


Type: peptide-like / Mass: 195.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13NO3
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 918 / 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: 55.14 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
Crystal growTemperature: 294 K / Method: microbatch
Details: 10 mM TrisCl, 100 mM NaCl, 50 mM HEPES, 10% PEG 3350, 2.5 mM Apstatin
PH range: 6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 29, 2016 / Details: Mirror
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 1.65→47.28 Å / Num. obs: 130822 / % possible obs: 98.8 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Net I/σ(I): 12.9
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.636 / Mean I/σ(I) obs: 2.2 / CC1/2: 0.742 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2152)refinement
Cootmodel building
PHENIXmodel building
PHASERphasing
Aimlessdata processing
XDSdata processing
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WL9

1wl9


Resolution: 1.65→30.983 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.58
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS AND I_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflectionSelection details
Rfree0.1775 6590 5.05 %random
Rwork0.154 ---
obs0.1552 130616 98.68 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.65→30.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6912 0 138 918 7968
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017280
X-RAY DIFFRACTIONf_angle_d1.0699869
X-RAY DIFFRACTIONf_dihedral_angle_d15.4924455
X-RAY DIFFRACTIONf_chiral_restr0.0681090
X-RAY DIFFRACTIONf_plane_restr0.0081282
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.66870.27122340.23474165X-RAY DIFFRACTION100
1.6687-1.68840.25722130.22824157X-RAY DIFFRACTION100
1.6884-1.7090.25152060.2124214X-RAY DIFFRACTION100
1.709-1.73060.2352190.20444178X-RAY DIFFRACTION100
1.7306-1.75340.2232240.19984179X-RAY DIFFRACTION100
1.7534-1.77740.22672050.19554155X-RAY DIFFRACTION100
1.7774-1.80280.21332270.19094153X-RAY DIFFRACTION100
1.8028-1.82970.22872160.18034169X-RAY DIFFRACTION100
1.8297-1.85830.20672420.17024195X-RAY DIFFRACTION100
1.8583-1.88870.18472150.16944148X-RAY DIFFRACTION100
1.8887-1.92130.20542010.16124216X-RAY DIFFRACTION100
1.9213-1.95620.19732050.16294163X-RAY DIFFRACTION100
1.9562-1.99380.18662210.15064183X-RAY DIFFRACTION100
1.9938-2.03450.17332110.15024207X-RAY DIFFRACTION100
2.0345-2.07880.19142150.15064126X-RAY DIFFRACTION100
2.0788-2.12710.16852420.14314153X-RAY DIFFRACTION99
2.1271-2.18030.16821980.14474177X-RAY DIFFRACTION99
2.1803-2.23920.18712250.14534159X-RAY DIFFRACTION99
2.2392-2.30510.1672040.14924158X-RAY DIFFRACTION99
2.3051-2.37950.17482300.15234121X-RAY DIFFRACTION99
2.3795-2.46450.1762290.15274134X-RAY DIFFRACTION99
2.4645-2.56310.18461970.1514131X-RAY DIFFRACTION98
2.5631-2.67970.1922620.15344094X-RAY DIFFRACTION99
2.6797-2.82090.18372380.15644098X-RAY DIFFRACTION98
2.8209-2.99750.15912320.15454070X-RAY DIFFRACTION97
2.9975-3.22870.19592210.1554039X-RAY DIFFRACTION96
3.2287-3.55320.16422280.1483973X-RAY DIFFRACTION95
3.5532-4.06640.14442000.13144031X-RAY DIFFRACTION96
4.0664-5.11950.13552190.12454075X-RAY DIFFRACTION96
5.1195-30.98860.1682110.16094005X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: -1.817 Å / Origin y: -6.699 Å / Origin z: 16.8222 Å
111213212223313233
T0.0852 Å2-0.0048 Å2-0.0008 Å2-0.1138 Å2-0.0069 Å2--0.0966 Å2
L0.2171 °2-0.0131 °2-0.0163 °2-0.6267 °20.0071 °2--0.2831 °2
S0.0122 Å °0.0036 Å °-0.0121 Å °-0.0229 Å °-0.0171 Å °0.0412 Å °0.0139 Å °-0.0158 Å °0.0094 Å °
Refinement TLS groupSelection details: all

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