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

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Basic information

Entry
Database: PDB / ID: 8zei
TitleCrystal structure of human cytosolic beta-alanyl lysine dipeptidase with crystal soaked in beta-alanyl histidine
ComponentsXaa-Arg dipeptidase
KeywordsHYDROLASE / Cytosolic / PM20D2 / metabolite / proofreading.
Function / homology
Function and homology information


Xaa-Arg dipeptidase / regulation of protein metabolic process / dipeptidase activity / 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 / HISTIDINE / 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 with crystal soaked in beta-alanyl histidine
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

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Assembly

Deposited unit
A: Xaa-Arg dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3018
Polymers49,7491
Non-polymers5527
Water1,63991
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)201,20432
Polymers198,9954
Non-polymers2,20928
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation3
MethodPISA
Unit cell
Length a, b, c (Å)79.477, 115.308, 124.100
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-661-

HOH

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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: 49748.809 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Catalyzes the peptide bond hydrolysis in dipeptides having the basic amino acids lysine, ornithine, or arginine at the C-terminus.
Source: (gene. exp.) Homo sapiens (human) / Gene: PM20D2, ACY1L2 / Plasmid: pST50STR / Details (production host): T7 promoter based / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IYS1, Xaa-Arg dipeptidase

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Non-polymers , 6 types, 98 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-HIS / HISTIDINE


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10N3O2 / 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 294.15 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: Nov 1, 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: 2.25→44.59 Å / Num. obs: 26439 / % possible obs: 99.9 % / Redundancy: 7.8 % / Biso Wilson estimate: 51.73 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.047 / Rrim(I) all: 0.134 / Net I/σ(I): 14.4
Reflection shellResolution: 2.25→2.32 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.533 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2394 / CC1/2: 0.626 / Rpim(I) all: 0.578 / % possible all: 99.9

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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→35.96 Å / SU ML: 0.2929 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.775
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2191 1257 4.89 %
Rwork0.2026 24435 -
obs0.2035 25692 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.24 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3003 0 30 91 3124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213145
X-RAY DIFFRACTIONf_angle_d0.50164290
X-RAY DIFFRACTIONf_chiral_restr0.0383467
X-RAY DIFFRACTIONf_plane_restr0.0039564
X-RAY DIFFRACTIONf_dihedral_angle_d6.2223441
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.390.3111210.29752690X-RAY DIFFRACTION99.96
2.39-2.50.32531460.27932669X-RAY DIFFRACTION99.93
2.5-2.630.35381230.26272693X-RAY DIFFRACTION99.96
2.63-2.80.28021390.26052671X-RAY DIFFRACTION99.93
2.8-3.010.25131250.23732727X-RAY DIFFRACTION99.96
3.01-3.320.27461250.22952725X-RAY DIFFRACTION99.96
3.32-3.80.2251700.19942677X-RAY DIFFRACTION100
3.8-4.780.1971480.16592741X-RAY DIFFRACTION99.97
4.78-350.16641600.12842X-RAY DIFFRACTION99.7
Refinement TLS params.Method: refined / Origin x: 7.63235657186 Å / Origin y: 21.8633570436 Å / Origin z: 29.9513227737 Å
111213212223313233
T0.343649701096 Å20.0121004061163 Å2-0.0193461636028 Å2-0.421744242025 Å2-0.00916350681115 Å2--0.445249630221 Å2
L0.523598300081 °20.448201895454 °20.297811867316 °2-1.51971258959 °21.82045225844 °2--3.10983836332 °2
S0.0769308008089 Å °-0.268875976247 Å °0.0520723118335 Å °0.0406692798756 Å °-0.000545942148887 Å °0.0688098298187 Å °0.107012796949 Å °-0.0677988173008 Å °-0.0846328089897 Å °
Refinement TLS groupSelection details: all

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