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- PDB-4lf0: The E142D mutant of the amidase from Geobacillus pallidus -

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Basic information

Entry
Database: PDB / ID: 4lf0
TitleThe E142D mutant of the amidase from Geobacillus pallidus
ComponentsAliphatic amidase
KeywordsHYDROLASE / alpha-beta-beta-alpha sandwich
Function / homology
Function and homology information


amidase / amidase activity
Similarity search - Function
Aliphatic amidase / : / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.1 Å
AuthorsSewell, B.T. / Weber, B.W. / Kimani, S.W. / Cowan, D.A. / Hunter, R. / Venter, G.A. / Gumbart, J.C. / Thuku, R.N. / Varsani, A.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The mechanism of the amidases: mutating the glutamate adjacent to the catalytic triad inactivates the enzyme due to substrate mispositioning.
Authors: Weber, B.W. / Kimani, S.W. / Varsani, A. / Cowan, D.A. / Hunter, R. / Venter, G.A. / Gumbart, J.C. / Sewell, B.T.
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aliphatic amidase


Theoretical massNumber of molelcules
Total (without water)38,6271
Polymers38,6271
Non-polymers00
Water6,936385
1
A: Aliphatic amidase
x 6


Theoretical massNumber of molelcules
Total (without water)231,7616
Polymers231,7616
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation14_445-y-1/2,-x-1/2,-z+1/21
crystal symmetry operation18_445-x-1/2,z-1/2,y+1/21
crystal symmetry operation22_445z-1/2,-y-1/2,x+1/21
Buried area43110 Å2
ΔGint-245 kcal/mol
Surface area51480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.633, 130.633, 130.633
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number208
Space group name H-MP4232
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

21A-460-

HOH

31A-507-

HOH

41A-771-

HOH

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Components

#1: Protein Aliphatic amidase / Acylamide amidohydrolase


Mass: 38626.805 Da / Num. of mol.: 1 / Mutation: E142D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus sp. (bacteria) / Strain: RAPc8 / Gene: ami, amiE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (2DE) / References: UniProt: Q9L543, amidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.4 Å3/Da / Density % sol: 48.85 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.7749 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 5, 2013 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.1→53.33 Å / Num. all: 152904 / Num. obs: 152140 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.101→1.106 Å / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 12.58

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Processing

Software
NameClassification
MAR345dtbdata collection
REFMACrefinement
XDSdata reduction
XDSdata scaling
REFMACphasing
RefinementResolution: 1.1→53.33 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.262 / SU ML: 0.013 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13749 7607 5 %RANDOM
Rwork0.13078 ---
obs0.13112 144532 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 6.992 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.1→53.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2649 0 0 385 3034
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0192821
X-RAY DIFFRACTIONr_bond_other_d0.0010.022657
X-RAY DIFFRACTIONr_angle_refined_deg2.2771.9483839
X-RAY DIFFRACTIONr_angle_other_deg2.10436155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4585369
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8624.656131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.46815493
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0851514
X-RAY DIFFRACTIONr_chiral_restr0.1290.2411
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213253
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02645
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.101→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.171 552 -
Rwork0.156 10491 -
obs--99.41 %

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