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- PDB-2ioh: Crystal structure of phosphonoacetaldehyde hydrolase with a K53R ... -

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Basic information

Entry
Database: PDB / ID: 2ioh
TitleCrystal structure of phosphonoacetaldehyde hydrolase with a K53R mutation
ComponentsPhosphonoacetaldehyde hydrolase
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 / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...Phosphonoacetaldehyde hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / haloacid dehalogenase-like hydrolase / 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: 2.9 Å
AuthorsAllen, K.A. / Lahiri, S.D. / Zhang, G. / Dunaway-Mariano, D. / Peisach, E.
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 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphonoacetaldehyde hydrolase
B: Phosphonoacetaldehyde hydrolase
C: Phosphonoacetaldehyde hydrolase
D: Phosphonoacetaldehyde hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,57312
Polymers122,0964
Non-polymers4778
Water1,44180
1
A: Phosphonoacetaldehyde hydrolase
B: Phosphonoacetaldehyde hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2876
Polymers61,0482
Non-polymers2394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Phosphonoacetaldehyde hydrolase
hetero molecules

C: Phosphonoacetaldehyde hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2876
Polymers61,0482
Non-polymers2394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
MethodPISA
3
D: Phosphonoacetaldehyde hydrolase
hetero molecules

D: Phosphonoacetaldehyde hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2876
Polymers61,0482
Non-polymers2394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
MethodPISA
Unit cell
Length a, b, c (Å)251.728, 251.728, 156.340
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein
Phosphonoacetaldehyde hydrolase


Mass: 30524.082 Da / Num. of mol.: 4 / Mutation: K53R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: O31156
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 3.9 Å3/Da / Density % sol: 68.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Ammonium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5 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: 1.5 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. all: 51994 / Num. obs: 50000 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.12

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→50 Å / SU B: 14.156 / SU ML: 0.274 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.578 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The structure was refined using strict NCS constraints
RfactorNum. reflection% reflectionSelection details
Rfree0.265 4000 9.5 %RANDOM
Rwork0.253 ---
all-39598 --
obs-39598 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK / Bsol: 68.198 Å2
Displacement parametersBiso mean: 48.192 Å2
Baniso -1Baniso -2Baniso -3
1-0.449 Å2-7.144 Å20 Å2
2--0.449 Å20 Å2
3----0.898 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8164 0 24 80 8268
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.511
X-RAY DIFFRACTIONc_mcbond_it1.2891.5
X-RAY DIFFRACTIONc_scbond_it2.0572
X-RAY DIFFRACTIONc_mcangle_it2.2512
X-RAY DIFFRACTIONc_scangle_it3.3932.5
LS refinement shellResolution: 2.9→3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.389 1263 -
obs--73.82 %

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