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- PDB-2vqr: Crystal structure of a phosphonate monoester hydrolase from rhizo... -

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Basic information

Entry
Database: PDB / ID: 2vqr
TitleCrystal structure of a phosphonate monoester hydrolase from rhizobium leguminosarum: a new member of the alkaline phosphatase superfamily
ComponentsPUTATIVE SULFATASE
KeywordsHYDROLASE / PHOSPHONATE MONOESTER HYDROLASE / PLASMID / FORMYLGLYCINE / PHOSPHODIESTERASE / ALKALINE PHOSPHATASE SUPERFAMILY
Function / homology
Function and homology information


sulfuric ester hydrolase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3360 / N-sulphoglucosamine sulphohydrolase, C-terminal / N-sulphoglucosamine sulphohydrolase, C-terminal / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3360 / N-sulphoglucosamine sulphohydrolase, C-terminal / N-sulphoglucosamine sulphohydrolase, C-terminal / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Multifunctional alkaline phosphatase superfamily protein pRL90232
Similarity search - Component
Biological speciesRHIZOBIUM LEGUMINOSARUM BV. VICIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 Å
AuthorsJonas, S. / Hyvonen, M. / Hollfelder, F.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: A New Member of the Alkaline Phosphatase Superfamily with a Formylglycine Nucleophile: Structural and Kinetic Characterisation of a Phosphonate Monoester Hydrolase/Phosphodiesterase from Rhizobium Leguminosarum.
Authors: Jonas, S. / Van Loo, B. / Hyvonen, M. / Hollfelder, F.
History
DepositionMar 18, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Apr 24, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_proc ...entity_poly / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PUTATIVE SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3356
Polymers61,0981
Non-polymers2365
Water11,638646
1
A: PUTATIVE SULFATASE
hetero molecules

A: PUTATIVE SULFATASE
hetero molecules

A: PUTATIVE SULFATASE
hetero molecules

A: PUTATIVE SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,33824
Polymers244,3944
Non-polymers94420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area19580 Å2
ΔGint-62.8 kcal/mol
Surface area80210 Å2
MethodPQS
Unit cell
Length a, b, c (Å)59.700, 96.600, 178.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2618-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PUTATIVE SULFATASE / / PHOSPHONATE MONOESTER HYDROLASE


Mass: 61098.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RHIZOBIUM LEGUMINOSARUM BV. VICIAE (bacteria)
Strain: 3841 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 TUNER / References: UniProt: Q1M964

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Non-polymers , 5 types, 651 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 646 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsMANGANESE (II) ION (MN): TYPE OF METAL ION AND OCCUPANCY WERE ASSIGNED ON THE BASIS OF MICROPIXE ...MANGANESE (II) ION (MN): TYPE OF METAL ION AND OCCUPANCY WERE ASSIGNED ON THE BASIS OF MICROPIXE DATA AND VALENCE BOND CALCULATIONS CALCIUM ION (CA): TYPE OF METAL ION AND OCCUPANCY WERE ASSIGNED ON THE BASIS OF MICROPIXE DATA AND VALENCE BOND CALCULATIONS
Sequence detailsRESIDUES 1-29 IN THE SEQUENCE ORIGINATE FROM A STREP-TAG AND A LINKER, THE ENZYME SEQUENCE STARTS ...RESIDUES 1-29 IN THE SEQUENCE ORIGINATE FROM A STREP-TAG AND A LINKER, THE ENZYME SEQUENCE STARTS WITH RESIDUE MET30 RESIDUE 57 IS A CASE OF MICROHETEROGENEITY WHERE MORE THAN ONE IDENTITY IS OBSERVED FOR A PARTICULAR RESIDUE NUMBER. AT POSITION 57 OF THE PROTEIN CHAIN A, BOTH DDZ AND CYS ARE PRESENT AT 0.60 AND 0.40 OCCUPANCIES RESPECTIVELY.

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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: 2.11 Å3/Da / Density % sol: 41.7 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1M TRIS-HCL PH 8.5, 25% PEG 4000, 0.2M SODIUM ACETATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9537
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.42→44.63 Å / Num. obs: 96695 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.7
Reflection shellResolution: 1.42→1.51 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.83 / % possible all: 93.5

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Processing

Software
NameVersionClassification
REFMAC5.4.0069refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.42→44.63 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.42 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.182 4891 5.1 %RANDOM
Rwork0.156 ---
obs0.157 91803 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.31 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20 Å20 Å2
2---1.27 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.42→44.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 11 646 4711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d
X-RAY DIFFRACTIONr_bond_other_d00.022896
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.9615755
X-RAY DIFFRACTIONr_angle_other_deg0.9936975
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5925522
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09722.701211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.95115633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4941539
X-RAY DIFFRACTIONr_chiral_restr0.1340.2605
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02937
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_it1.8681.52587
X-RAY DIFFRACTIONr_mcbond_other0.7141.51033
X-RAY DIFFRACTIONr_mcangle_it2.64924158
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.38331635
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6694.51591
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: 1.42→1.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.348 307
Rwork0.326 5899

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