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- PDB-2dyu: Helicobacter pylori formamidase AmiF contains a fine-tuned cystei... -

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Basic information

Entry
Database: PDB / ID: 2dyu
TitleHelicobacter pylori formamidase AmiF contains a fine-tuned cysteine-glutamate-lysine catalytic triad
ComponentsFormamidase
KeywordsHYDROLASE / Formamidase / AmiF / CEK / catalytic triad / Helicobacter pylori / aliphatic amidase
Function / homology
Function and homology information


formamidase / formamidase activity / N-carbamoylputrescine amidase activity / putrescine biosynthetic process from arginine
Similarity search - Function
Formamidase / : / 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 speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsWang, W.C. / Hung, C.L.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structure of Helicobacter pylori formamidase AmiF reveals a cysteine-glutamate-lysine catalytic triad
Authors: Hung, C.-L. / Liu, J.-H. / Chiu, W.-C. / Huang, S.-W. / Hwang, J.-K. / Wang, W.-C.
History
DepositionSep 18, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Formamidase
B: Formamidase


Theoretical massNumber of molelcules
Total (without water)74,6612
Polymers74,6612
Non-polymers00
Water12,845713
1
A: Formamidase
B: Formamidase

A: Formamidase
B: Formamidase

A: Formamidase
B: Formamidase


Theoretical massNumber of molelcules
Total (without water)223,9826
Polymers223,9826
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area31270 Å2
ΔGint-199.2 kcal/mol
Surface area58200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.215, 147.215, 72.273
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Formamidase / Formamide amidohydrolase


Mass: 37330.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Strain: 26695 / Gene: amiF / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: O25836, formamidase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M sodium cacodylate, 0.15M potassium thiocyanate, 20% polyethylene glycol 550 MME, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11131
21131
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL12B210.98
SYNCHROTRONSPring-8 BL12B220.9791
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDJul 11, 2004
ADSC QUANTUM 42CCDJul 11, 2004
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.981
20.97911
ReflectionResolution: 1.75→30 Å / Num. all: 58786 / Num. obs: 58786 / % possible obs: 99.7 % / Redundancy: 3.2 %
Reflection shellResolution: 1.75→1.81 Å / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.552 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21515 2960 5.1 %RANDOM
Rwork0.17433 ---
obs0.1764 55500 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5098 0 0 713 5811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225246
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0371.9497134
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5745642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.51424.298242
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27815838
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1811522
X-RAY DIFFRACTIONr_chiral_restr0.070.2742
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024074
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.32866
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3210.53568
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.51010
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.347
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.566
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6111.53270
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.06825144
X-RAY DIFFRACTIONr_scbond_it1.25732313
X-RAY DIFFRACTIONr_scangle_it2.024.51990
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 207 -
Rwork0.25 4016 -
obs--96.97 %

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