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- PDB-8xzc: Crystal structure of human cytosolic beta-alanyl lysine dipeptida... -

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Basic information

Entry
Database: PDB / ID: 8xzc
TitleCrystal structure of human cytosolic beta-alanyl lysine dipeptidase (PM20D2) Tyr314Phe mutant
ComponentsXaa-Arg dipeptidase
KeywordsHYDROLASE / PM20D2 / Carnosine / Proofreading / Cytosolic / Metabolite
Function / homology
Function and homology information


Xaa-Arg dipeptidase / dipeptidase activity / regulation of protein metabolic process / carboxypeptidase activity / proteolysis / nucleoplasm / identical protein binding
Similarity search - Function
Xaa-Arg dipeptidase / : / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40
Similarity search - Domain/homology
PHOSPHATE ION / Xaa-Arg dipeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsChandravanshi, K. / Kumar, A. / Makde, R.D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India) India
CitationJournal: To Be Published
Title: Crystal structure of human cytosolic beta-alanyl lysine dipeptidase (PM20D2) Tyr314Phe mutant
Authors: Chandravanshi, K. / Kumar, A. / Makde, R.D.
History
DepositionJan 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xaa-Arg dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0545
Polymers49,7331
Non-polymers3214
Water1,51384
1
A: Xaa-Arg dipeptidase
hetero molecules

A: Xaa-Arg dipeptidase
hetero molecules

A: Xaa-Arg dipeptidase
hetero molecules

A: Xaa-Arg dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,21420
Polymers198,9314
Non-polymers1,28316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
MethodPISA
Unit cell
Length a, b, c (Å)79.935, 115.526, 124.434
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-502-

PO4

21A-657-

HOH

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Components

#1: Protein Xaa-Arg dipeptidase / Beta-Ala-Lys dipeptidase


Mass: 49732.809 Da / Num. of mol.: 1 / Mutation: Y314F
Source method: isolated from a genetically manipulated source
Details: Human cytosolic beta-alanyl lysine dipeptidase (PM20D2)
Source: (gene. exp.) Homo sapiens (human) / Gene: PM20D2, ACY1L2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IYS1, Xaa-Arg dipeptidase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 4.6
Details: 70 mM calcium chloride, 35 mM sodium acetate pH4.6, 7% isopropanol, 15% glycerol, 20 mM Tris-Cl, and 200 mM NaCl (mixed in 1:1)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 5, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.35→45.19 Å / Num. obs: 24352 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 50.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.037 / Rrim(I) all: 0.105 / Net I/σ(I): 14.8
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 8.3 % / Rmerge(I) obs: 1.382 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2341 / CC1/2: 0.668 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→36.82 Å / SU ML: 0.287 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.623
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2399 1185 4.87 %
Rwork0.1956 23130 -
obs0.1979 24315 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.84 Å2
Refinement stepCycle: LAST / Resolution: 2.35→36.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 12 84 3094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313120
X-RAY DIFFRACTIONf_angle_d0.52954264
X-RAY DIFFRACTIONf_chiral_restr0.0399465
X-RAY DIFFRACTIONf_plane_restr0.0044561
X-RAY DIFFRACTIONf_dihedral_angle_d4.4771434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.460.32741330.2652842X-RAY DIFFRACTION99.93
2.46-2.590.29171190.24852888X-RAY DIFFRACTION99.9
2.59-2.750.3421580.25432858X-RAY DIFFRACTION99.7
2.75-2.960.30611450.23432863X-RAY DIFFRACTION99.9
2.96-3.260.23921730.22082849X-RAY DIFFRACTION100
3.26-3.730.26181310.20592903X-RAY DIFFRACTION99.77
3.73-4.70.20791560.16052933X-RAY DIFFRACTION100
4.7-36.820.20951700.1732994X-RAY DIFFRACTION99.18
Refinement TLS params.Method: refined / Origin x: 7.67408003436 Å / Origin y: 21.8270640053 Å / Origin z: 30.0242687056 Å
111213212223313233
T0.291699212214 Å20.00638647593916 Å2-0.0197777236864 Å2-0.391044265209 Å2-0.0154891540216 Å2--0.388718455902 Å2
L0.603787822335 °20.541734631069 °20.33082462673 °2-1.68692789389 °21.74296694683 °2--3.1550647366 °2
S0.0876085431687 Å °-0.252619527073 Å °0.110341878981 Å °0.104343677302 Å °-0.0282931243184 Å °0.0933442467944 Å °0.0660357447423 Å °-0.103256663936 Å °-0.0599929071513 Å °
Refinement TLS groupSelection details: all

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