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- PDB-7yh4: Crystal structure of human cytosolic beta-alanyl lysine dipeptida... -

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Basic information

Entry
Database: PDB / ID: 7yh4
TitleCrystal structure of human cytosolic beta-alanyl lysine dipeptidase (PM20D2)
ComponentsXaa-Arg dipeptidase
KeywordsHYDROLASE / Dipeptidase / carnosine proofreading / DNA repair
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsChandravanshi, K. / Gaur, N.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)
Authors: Chandravanshi, K. / Gaur, N.K. / Kumar, A. / Makde, R.D.
History
DepositionJul 12, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)49,8803
Polymers49,7491
Non-polymers1312
Water1,71195
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)199,51912
Polymers198,9954
Non-polymers5238
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area11240 Å2
ΔGint-377 kcal/mol
Surface area58490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.834, 112.888, 123.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-683-

HOH

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Components

#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
Source: (gene. exp.) Homo sapiens (human) / Gene: PM20D2, ACY1L2 / Plasmid: PST50STRN / Details (production host): T7-based / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: Q8IYS1, Xaa-Arg dipeptidase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.76 Å3/Da / Density % sol: 56.06 % / Description: Hexagonal
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: Y
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.987 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 13, 2021 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.03→44.59 Å / Num. obs: 35868 / % possible obs: 100 % / Redundancy: 7.2 % / Biso Wilson estimate: 42.23 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.02 / Rrim(I) all: 0.053 / Net I/σ(I): 23.3
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2616 / CC1/2: 0.69 / Rpim(I) all: 0.54 / % possible all: 99.8
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RAM

3ram


Resolution: 2.03→35.624 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 1783 4.98 %
Rwork0.1969 --
obs0.1989 35783 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.03→35.624 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3017 0 2 95 3114
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063133
X-RAY DIFFRACTIONf_angle_d0.7764281
X-RAY DIFFRACTIONf_dihedral_angle_d10.6221833
X-RAY DIFFRACTIONf_chiral_restr0.049464
X-RAY DIFFRACTIONf_plane_restr0.005563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0301-2.0850.34971070.36012600X-RAY DIFFRACTION99
2.085-2.14630.2811390.28372597X-RAY DIFFRACTION100
2.1463-2.21560.35481430.2532562X-RAY DIFFRACTION100
2.2156-2.29470.45151360.36172546X-RAY DIFFRACTION98
2.2947-2.38660.27341390.21632579X-RAY DIFFRACTION100
2.3866-2.49520.25451430.20582612X-RAY DIFFRACTION100
2.4952-2.62670.23951350.19572609X-RAY DIFFRACTION100
2.6267-2.79120.23731410.20792595X-RAY DIFFRACTION100
2.7912-3.00660.23241300.20342602X-RAY DIFFRACTION100
3.0066-3.3090.29541390.20832635X-RAY DIFFRACTION100
3.309-3.78730.24341590.19422612X-RAY DIFFRACTION100
3.7873-4.76980.19221380.15952670X-RAY DIFFRACTION100
4.7698-35.620.18791340.17232781X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 7.628 Å / Origin y: 21.1855 Å / Origin z: 28.8788 Å
111213212223313233
T0.221 Å2-0.0165 Å2-0.0013 Å2-0.3784 Å2-0.0099 Å2--0.3699 Å2
L0.7869 °20.37 °20.746 °2-1.8445 °22.4899 °2--4.1977 °2
S-0.0254 Å °-0.3352 Å °0.0406 Å °0.1019 Å °0.0193 Å °0.0221 Å °0.0173 Å °-0.0575 Å °-0.0111 Å °
Refinement TLS groupSelection details: all

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