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- PDB-8je0: A novel amidohydrolase -

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Basic information

Entry
Database: PDB / ID: 8je0
TitleA novel amidohydrolase
ComponentsAmidase
KeywordsHYDROLASE
Function / homologyDeacetylase Atu3266-like / deacetylase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / Amidohydrolase family / Metal-dependent hydrolase, composite domain superfamily / Amidohydrolase-related / Metal-dependent hydrolase / Amidase
Function and homology information
Biological speciesKlebsiella sp. PCX (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMa, D. / Feng, R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32101371 China
CitationJournal: To Be Published
Title: A novel amidohydrolase catalyze the degradation of PAM by Klebsiella sp. PCX
Authors: Ma, D. / Feng, R.
History
DepositionMay 15, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amidase
B: Amidase
C: Amidase
D: Amidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,7949
Polymers170,4704
Non-polymers3245
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.050, 108.050, 341.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.541368393611, 0.530404278354, 0.652373791551), (0.536207053239, -0.815444550466, 0.218018763346), (0.647612738028, 0.231778960689, -0.725862421487)18.5680065596, -37.487238314, -13.259734059
2given(-0.847933137547, 0.165683580943, -0.503545772751), (0.18174608933, -0.801465275467, -0.569755887406), (-0.497973647157, -0.574632372241, 0.649476622759)88.3907502336, -14.8377773199, 21.7103723798
3given(-0.688531334484, -0.708845510031, -0.153175207988), (-0.709493015653, 0.614684984163, 0.344647691104), (-0.150147468085, 0.345977474921, -0.926150810978)72.5879047806, 26.5267826953, 25.1330046383

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Components

#1: Protein
Amidase


Mass: 42617.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella sp. PCX (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A9E8ZAQ2
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
Has ligand of interestN

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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: 2.92 Å3/Da / Density % sol: 57.91 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.8 M Sodium formate, pH 7.0, 0.03 M Potassium bromide, 6% w/v Polyethylene glycol monomethyl ether 2000.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.9→48.8 Å / Num. obs: 46043 / % possible obs: 100 % / Redundancy: 19.3 % / Biso Wilson estimate: 62.01 Å2 / Rmerge(I) obs: 0.179 / Net I/σ(I): 15.9
Reflection shellResolution: 2.9→3 Å / Rmerge(I) obs: 1.435 / Num. unique obs: 4458

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-30007.21data scaling
PDB_EXTRACT3.27data extraction
HKL-30007.21data reduction
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→45.65 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 1995 4.35 %
Rwork0.214 --
obs0.2156 45869 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.9→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10945 0 4 0 10949
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00311129
X-RAY DIFFRACTIONf_angle_d0.61415165
X-RAY DIFFRACTIONf_dihedral_angle_d5.5321606
X-RAY DIFFRACTIONf_chiral_restr0.0461811
X-RAY DIFFRACTIONf_plane_restr0.0041974
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.970.38941390.33523075X-RAY DIFFRACTION100
2.97-3.050.36221400.30713069X-RAY DIFFRACTION100
3.05-3.140.30711390.26383070X-RAY DIFFRACTION100
3.14-3.240.31161400.24773072X-RAY DIFFRACTION100
3.24-3.360.29561410.23793089X-RAY DIFFRACTION100
3.36-3.490.25831400.23993093X-RAY DIFFRACTION100
3.49-3.650.27171410.22273089X-RAY DIFFRACTION100
3.65-3.850.26681410.21123114X-RAY DIFFRACTION100
3.85-4.090.22311400.18633100X-RAY DIFFRACTION100
4.09-4.40.21941440.18193138X-RAY DIFFRACTION100
4.4-4.840.20021440.16123153X-RAY DIFFRACTION100
4.85-5.540.22011440.19683170X-RAY DIFFRACTION100
5.54-6.980.26621470.22863239X-RAY DIFFRACTION100
6.98-45.650.21771550.20923403X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 44.7898 Å / Origin y: -5.9047 Å / Origin z: 8.334 Å
111213212223313233
T0.3453 Å2-0.0908 Å2-0.0525 Å2-0.3687 Å20.0174 Å2--0.3797 Å2
L0.4131 °2-0.0598 °2-0.1724 °2-0.5777 °20.0152 °2--1.0692 °2
S-0.0461 Å °0.0235 Å °0.0107 Å °-0.0851 Å °0.1258 Å °0.0466 Å °0.1667 Å °-0.0433 Å °-0.0749 Å °
Refinement TLS groupSelection details: all

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