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- PDB-2w8s: CRYSTAL STRUCTURE OF A catalytically promiscuous PHOSPHONATE MONO... -

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Basic information

Entry
Database: PDB / ID: 2w8s
TitleCRYSTAL STRUCTURE OF A catalytically promiscuous PHOSPHONATE MONOESTER HYDROLASE FROM Burkholderia caryophylli
ComponentsPHOSPHONATE MONOESTER HYDROLASE
KeywordsHYDROLASE / FORMYLGLYCINE / PHOSPHODIESTERASE / ALKALINE PHOSPHATASE SUPERFAMILY / CATALYTIC PROMISCUITY / PHOSPHONATE MONOESTER HYDROLASE
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Sulfuric-ester hydrolases / sulfuric ester hydrolase activity / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / Hydrolases; Acting on ester bonds; Phosphoric-diester hydrolases / Hydrolases; Acting on ester bonds / metal ion binding / identical protein binding / cytoplasm
Similarity search - Function
: / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3360 / 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 / 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
: / Multifunctional alkaline phosphatase superfamily protein PehA
Similarity search - Component
Biological speciesBURKHOLDERIA CARYOPHYLLI (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsJonas, S. / van Loo, B. / Hyvonen, M. / Hollfelder, F.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: An Efficient, Multiply Promiscuous Hydrolase in the Alkaline Phosphatase Superfamily.
Authors: Van Loo, B. / Jonas, S. / Babtie, A.C. / Benjdia, A. / Berteau, O. / Hyvonen, M. / Hollfelder, F.
#1: Journal: 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
DepositionJan 19, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 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_ncs_dom_lim
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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED. SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS ... SHEET DETERMINATION METHOD: AUTHOR PROVIDED. SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHONATE MONOESTER HYDROLASE
B: PHOSPHONATE MONOESTER HYDROLASE
C: PHOSPHONATE MONOESTER HYDROLASE
D: PHOSPHONATE MONOESTER HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,40723
Polymers244,8814
Non-polymers1,52619
Water14,736818
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19900 Å2
ΔGint-112 kcal/mol
Surface area65160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.700, 200.100, 211.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22C
13D
23C

NCS domain segments:

Component-ID: 1 / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ARGARGAA3 - 51432 - 543
21ARGARGCC3 - 51432 - 543
12THRTHRBB2 - 51431 - 543
22THRTHRCC2 - 51431 - 543
13THRTHRDD2 - 51431 - 543
23THRTHRCC2 - 51431 - 543

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(-0.7909, 0.5932, 0.1501), (0.597, 0.6941, 0.4023), (0.1345, 0.4078, -0.9031)29.54, -29.05, 78.35
2given(0.7983, -0.5979, -0.07245), (-0.598, -0.8012, 0.02249), (-0.07149, 0.02537, -0.9971)9.738, 19, 88.29
3given(-0.9982, 0.02551, -0.05386), (0.000287, -0.9017, -0.4323), (-0.0596, -0.4316, 0.9001)45.16, 26.31, 7.373

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
PHOSPHONATE MONOESTER HYDROLASE


Mass: 61220.293 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: AT POSITION 57 OF THE PROTEIN CHAINS A, B, C, D. BOTH CYS AND FGL ARE PRESENT AT 0.80 AND 0.20 OCCUPANCIES, RESPECTIVELY.
Source: (gene. exp.) BURKHOLDERIA CARYOPHYLLI (bacteria) / Strain: BG2952 / Plasmid: PASK-IBA5PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q45087

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Non-polymers , 5 types, 837 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 818 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details2-AMINOPROPANEDIOIC ACID (FGL): THE MODIFICATION IS INCOMPLETE. ZINC ION (ZN): NATURE AND OCCUPANCY ...2-AMINOPROPANEDIOIC ACID (FGL): THE MODIFICATION IS INCOMPLETE. ZINC ION (ZN): NATURE AND OCCUPANCY OF THE METAL IONS WERE DETERMINED BY MICROPIXE. FE (III) ION (FE): NATURE AND OCCUPANCY OF THE METAL IONS WERE DETERMINED BY MICROPIXE.
Sequence detailsRESIDUES 1-29 IN THE PROTEIN SEQUENCE ORIGINATE FROM THE STREP-TAG AND LINKER. AT POSITION 57 OF ...RESIDUES 1-29 IN THE PROTEIN SEQUENCE ORIGINATE FROM THE STREP-TAG AND LINKER. AT POSITION 57 OF THE PROTEIN CHAINS A, B, C, D. BOTH CYS AND FGL ARE PRESENT AT 0.80 AND 0.20 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: 2.5 Å3/Da / Density % sol: 50.8 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1 M MES PH 6.5, 20 % (W/V) PEG 5000 MME, 0.3 M (NH4)2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 4, 2006 / Details: CONFOCAL MAXFLUX
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→48.62 Å / Num. obs: 96059 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.49
Reflection shellResolution: 2.4→2.5 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.52 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VQR

2vqr


Resolution: 2.4→48.62 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 20.292 / SU ML: 0.2 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES - RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.239 4887 5.1 %RANDOM
Rwork0.182 ---
obs0.185 91070 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20 Å2
2---1.25 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16358 0 67 818 17243
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02116881
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211596
X-RAY DIFFRACTIONr_angle_refined_deg1.5541.95522942
X-RAY DIFFRACTIONr_angle_other_deg1.122327901
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55852045
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.50523.023860
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.357152594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.67115147
X-RAY DIFFRACTIONr_chiral_restr0.1160.22392
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02119051
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023682
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_it0.6261.510258
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.169216494
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.84936623
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9224.56447
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A6929loose positional0.275
12C6929loose positional0.275
21B6974loose positional0.265
22C6974loose positional0.265
31D6950loose positional0.265
32C6950loose positional0.265
11A6929loose thermal2.2210
12C6929loose thermal2.2210
21B6974loose thermal1.7710
22C6974loose thermal1.7710
31D6950loose thermal1.6110
32C6950loose thermal1.6110
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.353 303
Rwork0.298 6312
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.13410.1526-0.10460.5961-0.46340.56280.1484-0.06880.06990.3402-0.04580.177-0.27780.1336-0.10260.282-0.09610.14990.1373-0.04040.092327.121920.219670.8677
20.18280.11-0.0660.331-0.10750.51970.0279-0.0280.0260.060.02350.18030.04210.0612-0.05150.0450.00520.06180.05840.01850.144114.3428-22.571660.6711
30.13150.0706-0.07720.6002-0.07220.25270.0692-0.00870.0368-0.00550.0170.1482-0.03240.0637-0.08630.0382-0.01230.00890.0729-0.02150.082830.454229.621226.1255
40.15210.0838-0.12390.4958-0.14420.20820.00120.00740.0021-0.19640.05630.21240.07720.014-0.05750.1072-0.01-0.10410.0837-0.0050.113814.1884-11.884416.3087
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 514
2X-RAY DIFFRACTION2B2 - 514
3X-RAY DIFFRACTION3C2 - 514
4X-RAY DIFFRACTION4D2 - 514

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