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- PDB-1rqn: Phosphonoacetaldehyde hydrolase complexed with magnesium -

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Basic information

Entry
Database: PDB / ID: 1rqn
TitlePhosphonoacetaldehyde hydrolase complexed with magnesium
ComponentsPhosphonoacetaldehyde Hydrolase
KeywordsHYDROLASE / Schiff-base formation / acid/base catalysis / structural enzymology / HAD 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
Phosphonoacetaldehyde hydrolase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMorais, M.C. / Zhang, G. / Zhang, W. / Olsen, D.B. / Dunaway-Mariano, D. / Allen, K.N.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: X-ray crystallographic and site-directed mutagenesis analysis of the mechanism of Schiff-base formation in phosphonoacetaldehyde hydrolase catalysis
Authors: Morais, M.C. / Zhang, G. / Zhang, W. / Olsen, D.B. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionDec 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 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_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_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_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_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,0694
Polymers61,0202
Non-polymers492
Water72140
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-35 kcal/mol
Surface area22390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.130, 45.180, 63.640
Angle α, β, γ (deg.)90.00, 105.10, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121
DetailsThe biological assembly is the dimer in the asymmetric unit

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Components

#1: Protein Phosphonoacetaldehyde Hydrolase / / phosphonatase


Mass: 30510.094 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.55 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 298 K / pH: 7.4
Details: PEG 4000, Tris-HCl, magnesium chloride, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K, pH 7.40

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→45.34 Å / Num. obs: 13003 / % possible obs: 85 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 82.1 Å2
Reflection shellResolution: 2.8→2.98 Å / % possible all: 57.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→45.34 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 214011.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.277 1278 10.3 %RANDOM
Rwork0.246 ---
obs0.246 12399 85.1 %-
all-12399 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.3154 Å2 / ksol: 0.348237 e/Å3
Displacement parametersBiso mean: 61 Å2
Baniso -1Baniso -2Baniso -3
1--29.41 Å20 Å2-2.45 Å2
2--9.52 Å20 Å2
3---19.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 2.8→45.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4098 0 2 40 4140
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.47
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.421 120 9.3 %
Rwork0.385 1177 -
obs--53.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2CIS_PEPTIDE.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAM

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