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

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Basic information

Entry
Database: PDB / ID: 8zel
TitleCrystal structure of human cytosolic beta-alanyl lysine dipeptidase Tyr314Phe mutant with a crystal soaked in beta-alanyl ornithine
ComponentsXaa-Arg dipeptidase
KeywordsHYDROLASE / Cytosolic / PM20D2 / Metabolite / Proofreading.
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
ACETIC ACID / L-ornithine / Xaa-Arg dipeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsChandravanshi, K. / Kumar, A. / Makde, R.D.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Science & Technology (DST, India)IF190153 India
CitationJournal: To Be Published
Title: Crystal structure of human cytosolic beta-alanyl lysine dipeptidase Tyr314Phe mutant with a crystal soaked in beta-alanyl ornithine
Authors: Chandravanshi, K. / Kumar, A. / Makde, R.D.
History
DepositionMay 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 14, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xaa-Arg dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1786
Polymers49,7331
Non-polymers4455
Water1,76598
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)200,71224
Polymers198,9314
Non-polymers1,78120
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
Unit cell
Length a, b, c (Å)78.777, 112.894, 123.255
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-504-

TRS

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 49732.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Catalyzes the peptide bond hydrolysis in dipeptides having basic amino acids lysine, ornithine or arginine at C-terminus.
Source: (gene. exp.) Homo sapiens (human) / Gene: PM20D2, ACY1L2 / Plasmid: pST44STR / Details (production host): T7 based promoter / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IYS1, Xaa-Arg dipeptidase

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Non-polymers , 5 types, 103 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ORN / L-ornithine


Type: L-peptide linking / Mass: 132.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 294 K / Method: microbatch / pH: 4.6
Details: 70 mM calcium chloride, 35 mM sodium acetate pH4.6, 7% isopropanol, 15% glycerol, 20mM Tris-Cl, 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: Oct 23, 2023
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.3→45.03 Å / Num. obs: 25710 / % possible obs: 100 % / Redundancy: 11 % / Biso Wilson estimate: 39.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.032 / Rrim(I) all: 0.107 / Net I/σ(I): 17.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 11.1 % / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2480 / CC1/2: 0.581 / Rpim(I) all: 0.589 / % 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: 2.3→36.43 Å / SU ML: 0.2636 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.9064
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2323 1315 4.98 %
Rwork0.194 25111 -
obs0.196 25710 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.53 Å2
Refinement stepCycle: LAST / Resolution: 2.3→36.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3012 0 23 98 3133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033131
X-RAY DIFFRACTIONf_angle_d0.53684269
X-RAY DIFFRACTIONf_chiral_restr0.0384462
X-RAY DIFFRACTIONf_plane_restr0.0044560
X-RAY DIFFRACTIONf_dihedral_angle_d4.6478437
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.33091480.29172730X-RAY DIFFRACTION99.76
2.34-2.450.32071500.26782743X-RAY DIFFRACTION99.97
2.45-2.580.32461290.24412777X-RAY DIFFRACTION99.9
2.58-2.740.25051420.2222764X-RAY DIFFRACTION99.93
2.74-2.950.27861410.20932774X-RAY DIFFRACTION99.93
2.95-3.240.2471500.19622774X-RAY DIFFRACTION100
3.24-3.710.21311640.17922791X-RAY DIFFRACTION100
3.71-4.680.21741430.15972827X-RAY DIFFRACTION99.97
4.68-36.430.18471480.18212931X-RAY DIFFRACTION99.68
Refinement TLS params.Method: refined / Origin x: -7.67783368155 Å / Origin y: -21.3015615144 Å / Origin z: -32.5648736161 Å
111213212223313233
T0.239431872526 Å2-0.00641775096487 Å2-0.00309386575125 Å2-0.384158792127 Å2-0.00274991026786 Å2--0.305990959715 Å2
L0.310879186813 °20.0447192125337 °2-0.192001913319 °2-1.0627206316 °2-1.39964339294 °2--2.52590105784 °2
S-0.0462980955117 Å °-0.133635798514 Å °-0.0337095682361 Å °0.0352461291302 Å °0.043432422055 Å °-0.0275768203123 Å °-0.0170952718836 Å °0.0162613523274 Å °-0.0155687322558 Å °
Refinement TLS groupSelection details: all

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