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- PDB-2iof: Crystal structure of phosphonoacetaldehyde hydrolase with sodium ... -

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Basic information

Entry
Database: PDB / ID: 2iof
TitleCrystal structure of phosphonoacetaldehyde hydrolase with sodium borohydride-reduced substrate intermediate
Components(Phosphonoacetaldehyde hydrolase) x 2
KeywordsHYDROLASE / Phosphonoacetaldehyde hydrolase / Haloacid dehalogenase superfamily
Function / homology
Function and homology information


phosphonoacetaldehyde hydrolase / phosphonoacetaldehyde hydrolase activity / organic phosphonate catabolic process / magnesium ion binding
Similarity search - Function
Phosphonoacetaldehyde hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 ...Phosphonoacetaldehyde hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phosphonoacetaldehyde hydrolase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAllen, K.A. / Lahiri, S.D. / Zhang, G. / Dunaway-Mariano, D.
CitationJournal: Bioorg.Chem. / Year: 2006
Title: Diversification of function in the haloacid dehalogenase enzyme superfamily: The role of the cap domain in hydrolytic phosphoruscarbon bond cleavage.
Authors: Lahiri, S.D. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionOct 10, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Remark 999 SEQUENCE AUTHORS STATE THAT THE ETHYLATION OF THE LYSINE AT SEQUENCE POSITION 53 IN CHAIN K ... SEQUENCE AUTHORS STATE THAT THE ETHYLATION OF THE LYSINE AT SEQUENCE POSITION 53 IN CHAIN K OCCURED SPONTANEOUSLY DURING CRYSTALLIZATION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphonoacetaldehyde hydrolase
K: Phosphonoacetaldehyde hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2586
Polymers61,0192
Non-polymers2394
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-53 kcal/mol
Surface area24290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.820, 64.020, 98.330
Angle α, β, γ (deg.)90.00, 123.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Phosphonoacetaldehyde hydrolase /


Mass: 30496.070 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O31156
#2: Protein Phosphonoacetaldehyde hydrolase /


Mass: 30523.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O31156
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 3.44 Å3/Da / Density % sol: 64.28 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5621 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 3, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5621 Å / Relative weight: 1
ReflectionResolution: 2.4→100 Å / Num. all: 28942 / Num. obs: 27942 / % possible obs: 92.8 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.19

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
DENZOdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→100 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.298 1945 6.7 %
Rwork0.231 --
obs0.231 19784 68.4 %
Solvent computationBsol: 39.692 Å2
Displacement parametersBiso mean: 27.979 Å2
Baniso -1Baniso -2Baniso -3
1-0.257 Å20 Å2-8.3 Å2
2--5.946 Å20 Å2
3----6.203 Å2
Refinement stepCycle: LAST / Resolution: 2.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4082 0 12 349 4443
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.654
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.2061.5
X-RAY DIFFRACTIONc_mcangle_it2.0382
X-RAY DIFFRACTIONc_scbond_it1.6732
X-RAY DIFFRACTIONc_scangle_it2.7022.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_edit_Final.paramprotein_edit.top
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION3CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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