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- PDB-2plq: Crystal structure of the amidase from geobacillus pallidus RAPc8 -

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Basic information

Entry
Database: PDB / ID: 2plq
TitleCrystal structure of the amidase from geobacillus pallidus RAPc8
ComponentsAliphatic amidase
KeywordsHYDROLASE / Nitrilase fold / alpha-beta-beta-alpha
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 superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGeobacillus pallidus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsKimani, S.W. / Sewell, B.T. / Agarkar, V.B. / Sayed, M.F. / Cowan, D.A.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing.
Authors: Agarkar, V.B. / Kimani, S.W. / Cowan, D.A. / Sayed, M.F. / Sewell, B.T.
#1: Journal: Thesis / Year: 2007
Title: The Crystal Structure of an aliphatic amidase from Geobacillus pallidus RAPc8
Authors: Kimani, S.W.
#2: Journal: To be Published
Title: The Crystal Structure of an aliphatic amidase from Geobacillus pallidus RAPc8
History
DepositionApr 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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
Remark 999SEQUENCE The source organism is listed in GenBank entry AAO23013 and UNP entry Q9L543 as Bacillus ...SEQUENCE The source organism is listed in GenBank entry AAO23013 and UNP entry Q9L543 as Bacillus sp. It is correctly classified by its 16S RNA sequence as Geobacillus pallidus.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aliphatic amidase


Theoretical massNumber of molelcules
Total (without water)38,6411
Polymers38,6411
Non-polymers00
Water5,495305
1
A: Aliphatic amidase
x 6


Theoretical massNumber of molelcules
Total (without water)231,8456
Polymers231,8456
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation13_544y+1/2,x-1/2,-z-1/21
crystal symmetry operation19_544-x+1/2,-z-1/2,-y-1/21
crystal symmetry operation22_544z+1/2,-y-1/2,x-1/21
Buried area43030 Å2
ΔGint-243 kcal/mol
Surface area51770 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)130.398, 130.398, 130.398
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-1038-

HOH

21A-1050-

HOH

31A-1083-

HOH

41A-1108-

HOH

51A-1158-

HOH

61A-1305-

HOH

DetailsFour biological assemblies are generated by applying the space group symmetry operators. Our nomenclature A,B,C,D,E,F refers to a hexamer generated as follows: A -x, y, -z B -z+1/2, -y+1/2, -x+1/2 C y, z, x D -y+1/2, x+1/2, z+1/2 E z, -x, -y F x+1/2, -z+1/2, y+1/2

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Components

#1: Protein Aliphatic amidase / Acylamide amidohydrolase


Mass: 38640.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus pallidus (bacteria) / Strain: RAPc8 / Gene: amiE, ami / Plasmid: pNH223 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9L543, amidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.41 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: The purified enzyme was concentrated to 10 mg ml-1 and then crystallized with 1.2 M sodium citrate, 400 mM NaCl, 100 mM sodium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 6, 2005 / Details: AXCO PX50 0.1mm focus
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 30300 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 7.9 % / Biso Wilson estimate: 12.7 Å2 / Rmerge(I) obs: 0.111 / Χ2: 1.038 / Net I/σ(I): 8.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.315 / Mean I/σ(I) obs: 3.23 / Num. unique all: 2824 / Rsym value: 0.315 / Χ2: 0.591 / % possible all: 94.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
CrystalClear(MSC/RIGAKU)data collection
PHASERphasing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1j31 with non-identical side chains replaced by alanine.

1j31


Resolution: 1.9→46.13 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.104 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Density sufficient to accommodate two additional atoms connected to the sulfur of Cys 166 was observed in the active site. This density was ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Density sufficient to accommodate two additional atoms connected to the sulfur of Cys 166 was observed in the active site. This density was interpreted to indicate oxidation of the cysteine to sulfinic acid but this was not confirmed and co-ordinates of these atoms are not included in the deposition.
RfactorNum. reflection% reflectionSelection details
Rfree0.177 1501 5 %RANDOM
Rwork0.146 ---
all0.147 30253 --
obs0.147 30253 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.557 Å2
Refinement stepCycle: LAST / Resolution: 1.9→46.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2650 0 0 305 2955
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.013
X-RAY DIFFRACTIONr_angle_refined_deg1.29
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.759
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.307
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.259
X-RAY DIFFRACTIONr_chiral_restr0.091
X-RAY DIFFRACTIONr_gen_planes_refined0.005
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 86 -
Rwork0.176 1978 -
obs-2064 93.69 %

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