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- PDB-1rdf: G50P mutant of phosphonoacetaldehyde hydrolase in complex with su... -

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Basic information

Entry
Database: PDB / ID: 1rdf
TitleG50P mutant of phosphonoacetaldehyde hydrolase in complex with substrate analogue vinyl sulfonate
Componentsphosphonoacetaldehyde hydrolase
KeywordsHYDROLASE / haloacid dehalogenase / specificity loop / phosphonatase / Schiff-base
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
ETHANESULFONIC ACID / Phosphonoacetaldehyde hydrolase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLahiri, S.D. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N.
CitationJournal: Biochemistry / Year: 2004
Title: Analysis of the substrate specificity loop of the HAD superfamily cap domain
Authors: Lahiri, S.D. / Zhang, G. / Dai, J. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionNov 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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_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
Revision 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
E: phosphonoacetaldehyde hydrolase
F: phosphonoacetaldehyde hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,10818
Polymers183,3016
Non-polymers80712
Water5,152286
1
A: phosphonoacetaldehyde hydrolase
C: phosphonoacetaldehyde hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3696
Polymers61,1002
Non-polymers2694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: phosphonoacetaldehyde hydrolase
D: phosphonoacetaldehyde hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3696
Polymers61,1002
Non-polymers2694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-31 kcal/mol
Surface area23930 Å2
MethodPISA
3
E: phosphonoacetaldehyde hydrolase
F: phosphonoacetaldehyde hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3696
Polymers61,1002
Non-polymers2694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: phosphonoacetaldehyde hydrolase
F: phosphonoacetaldehyde hydrolase
hetero molecules

E: phosphonoacetaldehyde hydrolase
F: phosphonoacetaldehyde hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,73812
Polymers122,2014
Non-polymers5388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area7850 Å2
ΔGint-73 kcal/mol
Surface area44420 Å2
MethodPISA
5
A: phosphonoacetaldehyde hydrolase
hetero molecules

B: phosphonoacetaldehyde hydrolase
C: phosphonoacetaldehyde hydrolase
D: phosphonoacetaldehyde hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,73812
Polymers122,2014
Non-polymers5388
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation2_655-x+1,y,-z1
identity operation1_555x,y,z1
Buried area8210 Å2
ΔGint-69 kcal/mol
Surface area45020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.714, 147.348, 131.308
Angle α, β, γ (deg.)90.00, 125.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
phosphonoacetaldehyde hydrolase /


Mass: 30550.156 Da / Num. of mol.: 6 / Mutation: G50P
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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ESA / ETHANESULFONIC ACID / Ethanesulfonic acid


Mass: 110.132 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O3S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 3.92 Å3/Da / Density % sol: 68.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.2M ammonium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2002
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.7→100 Å / Num. obs: 53643 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 26.3 Å2 / Rmerge(I) obs: 0.29 / Rsym value: 0.28 / Net I/σ(I): 10.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 3 % / Rmerge(I) obs: 0.393 / Mean I/σ(I) obs: 2.5 / Num. unique all: 77509 / Rsym value: 0.23 / % possible all: 56

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FEZ

1fez


Resolution: 2.8→34.09 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 361966.02 / Data cutoff high rms absF: 361966.02 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 5437 10.1 %RANDOM
Rwork0.23 ---
all0.24 59080 --
obs0.23 53643 77.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.8633 Å2 / ksol: 0.317618 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1-2.36 Å20 Å216.21 Å2
2---7.48 Å20 Å2
3---5.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.86 Å0.72 Å
Refinement stepCycle: LAST / Resolution: 2.8→34.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12599 0 42 286 12927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_improper_angle_d0.88
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.446 681 10.2 %
Rwork0.371 6025 -
obs--58 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4VSO.PARAMVSO.TOP

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