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- PDB-4as3: Pseudomonas Aeruginosa Phosphorylcholine Phosphatase. Orthorhombi... -

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Basic information

Entry
Database: PDB / ID: 4as3
TitlePseudomonas Aeruginosa Phosphorylcholine Phosphatase. Orthorhombic 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
Phosphorylcholine phosphatase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)150,85622
Polymers148,5254
Non-polymers2,33118
Water7,368409
1
A: PHOSPHORYLCHOLINE PHOSPHATASE
B: PHOSPHORYLCHOLINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,42811
Polymers74,2622
Non-polymers1,1669
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-40.9 kcal/mol
Surface area25090 Å2
MethodPISA
2
C: PHOSPHORYLCHOLINE PHOSPHATASE
D: PHOSPHORYLCHOLINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,42811
Polymers74,2622
Non-polymers1,1669
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5970 Å2
ΔGint-46.5 kcal/mol
Surface area25540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.343, 69.591, 119.569
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11D-2031-

HOH

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Components

#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
#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-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence details22 FIRST AMINOACIDS 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: 2.34 Å3/Da / Density % sol: 47.41 % / Description: NONE
Crystal growDetails: 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)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.747091
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.747091 Å / Relative weight: 1
ReflectionResolution: 2.4→50.05 Å / Num. obs: 54739 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 20.7
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AS2

4as2


Resolution: 2.4→119.6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.464 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.109 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24947 2773 5.1 %RANDOM
Rwork0.17731 ---
obs0.18093 51930 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.779 Å2
Baniso -1Baniso -2Baniso -3
1-13.08 Å20 Å20 Å2
2--0.75 Å20 Å2
3----13.82 Å2
Refinement stepCycle: LAST / Resolution: 2.4→119.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10460 0 148 409 11017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0210853
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.771.97714746
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.48551304
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.62324.24500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.962151804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0391564
X-RAY DIFFRACTIONr_chiral_restr0.1140.21596
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0218228
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: 2.399→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 215 -
Rwork0.242 3670 -
obs--97.81 %

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