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- PDB-7cf6: Crystal structure of Beta-aspartyl dipeptidase from thermophilic ... -

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Basic information

Entry
Database: PDB / ID: 7cf6
TitleCrystal structure of Beta-aspartyl dipeptidase from thermophilic keratin degrading Fervidobacterium islandicum AW-1 in complex with beta-Asp-Leu dipeptide
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
Chem-FWO / DI(HYDROXYETHYL)ETHER / Isoaspartyl dipeptidase
Similarity search - Component
Biological speciesFervidobacterium islandicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 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 24, 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 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Isoaspartyl dipeptidase
A: Isoaspartyl dipeptidase
C: Isoaspartyl dipeptidase
D: Isoaspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,09029
Polymers171,3564
Non-polymers2,73425
Water2,216123
1
B: Isoaspartyl dipeptidase
A: Isoaspartyl dipeptidase
C: Isoaspartyl dipeptidase
D: Isoaspartyl dipeptidase
hetero molecules

B: Isoaspartyl dipeptidase
A: Isoaspartyl dipeptidase
C: Isoaspartyl dipeptidase
D: Isoaspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,18058
Polymers342,7138
Non-polymers5,46750
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x,-y,z1
Buried area35880 Å2
ΔGint-230 kcal/mol
Surface area98810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.609, 150.425, 151.996
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2212
Components on special symmetry positions
IDModelComponents
11D-521-

HOH

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Components

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Protein , 1 types, 4 molecules BACD

#1: Protein
Isoaspartyl dipeptidase


Mass: 42839.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fervidobacterium islandicum (bacteria) / Gene: NA23_08080 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: A0A1B0VPV0, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases

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Non-polymers , 5 types, 148 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-FWO / (2S)-2-[[(3S)-3-azanyl-4-oxidanyl-4-oxidanylidene-butanoyl]amino]-4-methyl-pentanoic acid


Mass: 246.260 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H18N2O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2% Tacismate pH 5.0, 0.1 M Sodium citrate pH 5.6, 16 % w/v Polyethylene glycol 3,350

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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: 0.98461 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 11, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98461 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 46521 / % possible obs: 99.7 % / Redundancy: 10 % / Rmerge(I) obs: 0.31 / Rpim(I) all: 0.1 / Rrim(I) all: 0.327 / Χ2: 0.99 / Net I/σ(I): 2.5 / Num. measured all: 466994
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.756.91.55223030.3680.6131.6740.85199.4
2.75-2.881.59922540.3790.5881.7070.87699.7
2.8-2.858.91.43123180.5170.51.5190.872100
2.85-2.919.61.28122650.6350.4311.3530.875100
2.91-2.979.81.17923150.7120.391.2430.918100
2.97-3.049.31.06123040.6940.3581.1220.89799.5
3.04-3.1210.10.93222940.8450.3030.9820.91299.7
3.12-3.2110.86123100.8720.2680.9030.93599.8
3.2-3.311.10.73922860.8630.2290.7740.95499.8
3.3-3.4110.61723130.9190.1930.6471.00499.8
3.4-3.5210.90.50723050.9270.1580.5321.06999.7
3.52-3.6610.80.41323300.9520.130.4341.08899.8
3.66-3.8310.60.3423420.9620.1080.3571.112100
3.83-4.039.40.28423050.9640.0950.31.13799.5
4.03-4.2911.10.23423220.9790.0730.2451.117100
4.29-4.62110.19223410.9860.060.2011.18299.8
4.62-5.0810.70.1823710.9860.0560.1881.12799.8
5.08-5.8110.10.18123390.9860.0580.1911.0198.9
5.81-7.3210.50.14823740.9910.0470.1560.88799.1
7.32-509.70.08925300.9970.0290.0940.82599.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CDH

7cdh


Resolution: 2.75→47.66 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.857 / SU B: 20.242 / SU ML: 0.379 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.493 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2783 1994 5.4 %RANDOM
Rwork0.1958 ---
obs0.2002 34968 77.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 160.97 Å2 / Biso mean: 46.931 Å2 / Biso min: 13.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.75→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11521 0 156 123 11800
Biso mean--76.02 30.89 -
Num. residues----1497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01311850
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711465
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.64215953
X-RAY DIFFRACTIONr_angle_other_deg1.1791.58826609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.76651485
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.6522.948536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.653152118
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6661557
X-RAY DIFFRACTIONr_chiral_restr0.0610.21586
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212996
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022327
LS refinement shellResolution: 2.75→2.822 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 35 -
Rwork0.322 658 -
all-693 -
obs--19.81 %

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