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- PDB-5xgx: Crystal structure of colwellia psychrerythraea strain 34H isoaspa... -

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Basic information

Entry
Database: PDB / ID: 5xgx
TitleCrystal structure of colwellia psychrerythraea strain 34H isoaspartyl dipeptidase E80Q mutant complexed with beta-isoaspartyl lysine
ComponentsIsoaspartyl dipeptidase
KeywordsHYDROLASE / Colwellia psychrerythraea / Isoaspartyl dipeptidase / IadA / beta-isoaspartyl lysine
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 / : / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll ...Peptidase M38, beta-aspartyl dipeptidase / : / Urease, subunit C; domain 1 / Urease, subunit C, domain 1 / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolases / Metal-dependent hydrolase / Roll / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
D-ASPARTIC ACID / D-LYSINE / Isoaspartyl dipeptidase
Similarity search - Component
Biological speciesColwellia psychrerythraea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.33 Å
AuthorsLee, J.H. / Lee, C.W. / Park, S.H.
CitationJournal: PLoS ONE / Year: 2017
Title: Crystal structure and functional characterization of an isoaspartyl dipeptidase (CpsIadA) from Colwellia psychrerythraea strain 34H.
Authors: Park, S.H. / Lee, C.W. / Lee, S.G. / Shin, S.C. / Kim, H.J. / Park, H. / Lee, J.H.
History
DepositionApr 18, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,34510
Polymers85,5252
Non-polymers8208
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-27 kcal/mol
Surface area28060 Å2
MethodPISA
2
A: Isoaspartyl dipeptidase
B: Isoaspartyl dipeptidase
hetero molecules

A: Isoaspartyl dipeptidase
B: Isoaspartyl dipeptidase
hetero molecules

A: Isoaspartyl dipeptidase
B: Isoaspartyl dipeptidase
hetero molecules

A: Isoaspartyl dipeptidase
B: Isoaspartyl dipeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)345,38140
Polymers342,1008
Non-polymers3,28132
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
Buried area30230 Å2
ΔGint-222 kcal/mol
Surface area92170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.878, 107.878, 155.879
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein Isoaspartyl dipeptidase


Mass: 42762.508 Da / Num. of mol.: 2 / Mutation: E80Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colwellia psychrerythraea (strain 34H / ATCC BAA-681) (bacteria)
Strain: 34H / ATCC BAA-681 / Gene: iadA, CPS_1869 / Production host: Escherichia coli (E. coli)
References: UniProt: Q484B6, Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-DAS / D-ASPARTIC ACID


Type: D-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4
#4: Chemical ChemComp-DLY / D-LYSINE


Type: D-peptide linking / Mass: 146.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

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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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Bis-Tris propane pH 7.0 1 M ammonium citrate tribasic pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.33→50.01 Å / Num. obs: 36407 / % possible obs: 97.1 % / Redundancy: 6.8 % / Net I/σ(I): 31.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data processing
HKL-2000data scaling
RefinementResolution: 2.33→50.01 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.989 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.328 / ESU R Free: 0.244 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24636 1910 5 %RANDOM
Rwork0.18886 ---
obs0.19177 36407 95.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.708 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å2-0 Å2-0 Å2
2--0.72 Å2-0 Å2
3----1.44 Å2
Refinement stepCycle: 1 / Resolution: 2.33→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5780 0 40 334 6154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195930
X-RAY DIFFRACTIONr_bond_other_d0.0020.025542
X-RAY DIFFRACTIONr_angle_refined_deg1.841.9638054
X-RAY DIFFRACTIONr_angle_other_deg1.0752.99812862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5035758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.19724.59244
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.28315970
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.9971528
X-RAY DIFFRACTIONr_chiral_restr0.1110.2936
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216620
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021140
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.173.7893044
X-RAY DIFFRACTIONr_mcbond_other3.1683.7883043
X-RAY DIFFRACTIONr_mcangle_it4.6335.6593798
X-RAY DIFFRACTIONr_mcangle_other4.6345.663799
X-RAY DIFFRACTIONr_scbond_it4.0384.2392886
X-RAY DIFFRACTIONr_scbond_other4.0384.2412887
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0716.1714257
X-RAY DIFFRACTIONr_long_range_B_refined8.27245.9816555
X-RAY DIFFRACTIONr_long_range_B_other8.24545.8126488
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.332→2.392 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 138 -
Rwork0.237 2705 -
obs--97.87 %

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