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- PDB-7cdh: Crystal structure of Betaaspartyl dipeptidase from thermophilic k... -

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Basic information

Entry
Database: PDB / ID: 7cdh
TitleCrystal structure of Betaaspartyl dipeptidase from thermophilic keratin degrading Fervidobacterium islandicum-AW-1
ComponentsIsoaspartyl dipeptidase
KeywordsMETAL BINDING PROTEIN / Aspartyldipeptidase / thermophilic / feather-degrading bacterial protein
Function / homology
Function and homology information


hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / beta-aspartyl-peptidase activity / metallopeptidase activity / proteolysis / metal ion binding / cytoplasm
Similarity search - Function
Peptidase M38, beta-aspartyl dipeptidase / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Isoaspartyl dipeptidase
Similarity search - Component
Biological speciesFervidobacterium islandicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsDhanasingh, I. / La, J.W. / Lee, D.W. / Lee, S.H.
CitationJournal: Front Mol Biosci / Year: 2020
Title: Functional Characterization of Primordial Protein Repair Enzyme M38 Metallo-Peptidase From Fervidobacterium islandicum AW-1.
Authors: La, J.W. / Dhanasingh, I. / Jang, H. / Lee, S.H. / Lee, D.W.
History
DepositionJun 19, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: 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
X: Isoaspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,39412
Polymers42,4071
Non-polymers98811
Water3,513195
1
X: Isoaspartyl dipeptidase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)347,15496
Polymers339,2528
Non-polymers7,90288
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area49190 Å2
ΔGint-792 kcal/mol
Surface area90810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.940, 143.940, 119.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11X-621-

HOH

21X-691-

HOH

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Components

#1: Protein Isoaspartyl dipeptidase


Mass: 42406.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fervidobacterium islandicum (bacteria) / Gene: NA23_08080 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1B0VPV0, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 195 / 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: 3.65 Å3/Da / Density % sol: 66.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Sodium acetate pH 4.6, 1 M Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 19156 / % possible obs: 97.7 % / Redundancy: 22.9 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.016 / Rrim(I) all: 0.074 / Χ2: 0.903 / Net I/σ(I): 7.9 / Num. measured all: 439332
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.6424.60.8249650.9630.1690.8410.827100
2.64-2.6924.60.7659470.9610.1590.7811.541100
2.69-2.7424.60.5579760.9770.1150.5690.833100
2.74-2.824.70.4179680.9850.0860.4250.839100
2.8-2.8624.60.3639560.9870.0750.3710.866100
2.86-2.9324.50.2739700.9930.0560.2790.862100
2.93-324.50.2379560.9930.0490.2420.886100
3-3.0824.50.1939720.9960.040.1980.87100
3.08-3.1724.30.1519710.9960.0310.1540.858100
3.17-3.2824.30.1269770.9980.0260.1290.86100
3.28-3.3924.10.1099670.9980.0230.1110.861100
3.39-3.5323.70.0949680.9980.020.0960.954100
3.53-3.6914.70.0986530.9970.0240.1011.00866.5
3.69-3.8819.80.0719100.9980.0160.0731.02694
3.88-4.1322.60.0579860.9990.0120.0580.95100
4.13-4.4522.50.0469800.9990.010.0470.84999.9
4.45-4.8922.50.0429950.9990.0090.0430.834100
4.89-5.622.10.04110030.9990.0090.0420.755100
5.6-7.0521.70.04110080.9990.0090.0420.73699.9
7.05-5017.50.04110280.9970.010.0430.93794.7

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 10NW

10nw


Resolution: 2.6→30.85 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 7.105 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 929 4.9 %RANDOM
Rwork0.1629 ---
obs0.1657 18040 96.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.13 Å2 / Biso mean: 43.226 Å2 / Biso min: 19.95 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.6→30.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2821 0 58 195 3074
Biso mean--84.89 49.31 -
Num. residues----367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132927
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172852
X-RAY DIFFRACTIONr_angle_refined_deg1.681.6353932
X-RAY DIFFRACTIONr_angle_other_deg1.3251.5776619
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6025366
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49722.672131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.30915523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6151515
X-RAY DIFFRACTIONr_chiral_restr0.0840.2391
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023181
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02572
LS refinement shellResolution: 2.601→2.669 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 69 -
Rwork0.225 1358 -
all-1427 -
obs--99.79 %

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