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- PDB-1fez: THE CRYSTAL STRUCTURE OF BACILLUS CEREUS PHOSPHONOACETALDEHYDE HY... -

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Basic information

Entry
Database: PDB / ID: 1fez
TitleTHE CRYSTAL STRUCTURE OF BACILLUS CEREUS PHOSPHONOACETALDEHYDE HYDROLASE COMPLEXED WITH TUNGSTATE, A PRODUCT ANALOG
ComponentsPHOSPHONOACETALDEHYDE HYDROLASE
KeywordsHYDROLASE / HAD-family alpha/beta core domain / Mg(II) binding site / 5-helix bundle
Function / homology
Function and homology information


phosphonoacetaldehyde hydrolase / phosphonoacetaldehyde hydrolase activity / organic phosphonate catabolic process / phosphoglycolate phosphatase activity / DNA repair / magnesium ion binding / cytosol
Similarity search - Function
Phosphonoacetaldehyde hydrolase / : / Haloacid dehalogenase-like 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 ...Phosphonoacetaldehyde hydrolase / : / Haloacid dehalogenase-like 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
TUNGSTATE(VI)ION / Phosphonoacetaldehyde hydrolase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsMorais, M.C. / Zhang, W. / Baker, A.S. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N.
Citation
Journal: Biochemistry / Year: 2000
Title: The crystal structure of bacillus cereus phosphonoacetaldehyde hydrolase: insight into catalysis of phosphorus bond cleavage and catalytic diversification within the HAD enzyme superfamily.
Authors: Morais, M.C. / Zhang, W. / Baker, A.S. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and Preliminary Crystallographic Analysis of Phosphonoacetaldehyde Hydrolase
Authors: Morais, M.C. / Baker, A.S. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionJul 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)117,24310
Polymers116,6504
Non-polymers5936
Water28816
1
A: PHOSPHONOACETALDEHYDE HYDROLASE
B: PHOSPHONOACETALDEHYDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6215
Polymers58,3252
Non-polymers2963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-33 kcal/mol
Surface area22530 Å2
MethodPISA
2
C: PHOSPHONOACETALDEHYDE HYDROLASE
D: PHOSPHONOACETALDEHYDE HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6215
Polymers58,3252
Non-polymers2963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1790 Å2
ΔGint-33 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.478, 45.778, 130.273
Angle α, β, γ (deg.)90.00, 104.97, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a dimer constructed from chain A and chain B. The conformations of each monomer in the dimer are different. The crystallographic tetramer is generated by a non-crystallographic translation of this dimer

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Components

#1: Protein
PHOSPHONOACETALDEHYDE HYDROLASE


Mass: 29162.453 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / References: UniProt: O31156
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: WO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.6 Å3/Da / Density % sol: 52.65 %
Crystal growTemperature: 291.14 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 4000, TRIS-HCl, magnesium chloride, , pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 291.14K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
230 %PEG40001reservoir
3100 mMTris-HCl1reservoir
4100 mM1reservoirMgCl2

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.196994
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Apr 30, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.196994 Å / Relative weight: 1
ReflectionResolution: 2.9→100 Å / Num. all: 38774 / Num. obs: 38774 / % possible obs: 93.7 % / Observed criterion σ(I): -1 / Redundancy: 2.42 % / Biso Wilson estimate: 16.54 Å2 / Rmerge(I) obs: 0.215 / Net I/σ(I): 6.56
Reflection shellResolution: 3→100 Å / Rmerge(I) obs: 0.63 / Num. unique all: 3461 / % possible all: 91
Reflection shell
*PLUS
% possible obs: 91 %

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Processing

Software
NameClassification
XTALVIEWrefinement
SOLVEphasing
DMmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementResolution: 3→100 Å / σ(F): 0 / Stereochemistry target values: Engh & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1739 -RANDOM
Rwork0.248 ---
all-17343 --
obs-17343 70.4 %-
Refinement stepCycle: LAST / Resolution: 3→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8164 0 14 16 8194
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.43
X-RAY DIFFRACTIONcns_dihedral_angles21.69
Software
*PLUS
Name: CNS / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.53
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04

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