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- PDB-4as2: Pseudomonas Aeruginosa Phosphorylcholine Phosphatase. Monoclinic form -

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Basic information

Entry
Database: PDB / ID: 4as2
TitlePseudomonas Aeruginosa Phosphorylcholine Phosphatase. Monoclinic form
ComponentsPHOSPHORYLCHOLINE PHOSPHATASE
KeywordsHYDROLASE / HAD SUPERFAMILY / ALKYLAMMONIUM COMPOUNDS
Function / homology
Function and homology information


phosphoethanolamine/phosphocholine phosphatase / periplasmic space / hydrolase activity / metal ion binding
Similarity search - Function
de novo design (two linked rop proteins) - #310 / : / de novo design (two linked rop proteins) / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / Phosphorylcholine phosphatase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.12 Å
AuthorsInfantes, L. / Otero, L.H. / Albert, A.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: The Structural Domains of Pseudomonas Aeruginosa Phosphorylcholine Phosphatase Cooperate in Substrate Hydrolysis: 3D Structure and Enzymatic Mechanism.
Authors: Infantes, L. / Otero, L.H. / Beassoni, P.R. / Boetsch, C. / Lisa, A.T. / Domenech, C.E. / Albert, A.
History
DepositionApr 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHORYLCHOLINE PHOSPHATASE
B: PHOSPHORYLCHOLINE PHOSPHATASE
C: PHOSPHORYLCHOLINE PHOSPHATASE
D: PHOSPHORYLCHOLINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)152,08833
Polymers148,5254
Non-polymers3,56329
Water14,664814
1
A: PHOSPHORYLCHOLINE PHOSPHATASE
B: PHOSPHORYLCHOLINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,19017
Polymers74,2622
Non-polymers1,92715
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-52.5 kcal/mol
Surface area24850 Å2
MethodPISA
2
C: PHOSPHORYLCHOLINE PHOSPHATASE
D: PHOSPHORYLCHOLINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,89816
Polymers74,2622
Non-polymers1,63614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-47.3 kcal/mol
Surface area24570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.006, 156.633, 71.816
Angle α, β, γ (deg.)90.00, 118.03, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1337-

IOD

21C-2007-

HOH

31C-2130-

HOH

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PHOSPHORYLCHOLINE PHOSPHATASE


Mass: 37131.242 Da / Num. of mol.: 4 / Fragment: RESIDUES 23-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Plasmid: PET15-PCHP / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): CODONPLUS
References: UniProt: Q9HTR2, phosphoethanolamine/phosphocholine phosphatase

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Non-polymers , 5 types, 843 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: I
#5: Chemical
ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 814 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details22 FIRST AMINO ACIDS ARE THE SIGNAL PEPTIDE

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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: 2.29 Å3/Da / Density % sol: 46.42 % / Description: NONE
Crystal growMethod: microbatch
Details: 1UL PROTEIN SOLUTION (10 MG ML-1) WAS MIXED WITH 2UL PRECIPITANT SOLUTION (0.1 M BIS-TRIS PH 5.5, 0.2 M MGCL2, 25% PEG 3350) MICROBATCH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 1.7117
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Oct 25, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7117 Å / Relative weight: 1
ReflectionResolution: 2.12→95.29 Å / Num. obs: 74828 / % possible obs: 99.5 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.6
Reflection shellResolution: 2.12→2.23 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.81 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALEdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.12→95.29 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.492 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21007 3788 5.1 %RANDOM
Rwork0.15434 ---
obs0.15715 71122 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.139 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å2-0.72 Å2
2--0.84 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.12→95.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10460 0 133 814 11407
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0210828
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0051.97514716
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.78451304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.9524.24500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.833151804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.991564
X-RAY DIFFRACTIONr_chiral_restr0.1870.21592
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218228
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 275 -
Rwork0.2 5167 -
obs--99.76 %

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