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- PDB-4upk: Phosphonate monoester hydrolase SpPMH from Silicibacter pomeroyi -

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Basic information

Entry
Database: PDB / ID: 4upk
TitlePhosphonate monoester hydrolase SpPMH from Silicibacter pomeroyi
ComponentsPHOSPHONATE MONOESTER HYDROLASE
KeywordsHYDROLASE / ALAKALINE PHOSPHATASE SUPERFAMILY / PROMISCUITY
Function / homology
Function and homology information


phosphoric ester hydrolase activity / phosphorus metabolic process / sulfuric ester hydrolase activity
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3360 / 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
Phosphonate monoester hydrolase, putative
Similarity search - Component
Biological speciesRUEGERIA POMEROYI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsValkov, E. / van Loo, B. / Hollfelder, F. / Hyvonen, M.
CitationJournal: J.Am.Chem.Soc. / Year: 2019
Title: Balancing Specificity and Promiscuity in Enzyme Evolution: Multidimensional Activity Transitions in the Alkaline Phosphatase Superfamily.
Authors: van Loo, B. / Bayer, C.D. / Fischer, G. / Jonas, S. / Valkov, E. / Mohamed, M.F. / Vorobieva, A. / Dutruel, C. / Hyvonen, M. / Hollfelder, F.
History
DepositionJun 17, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 2.0Dec 19, 2018Group: Atomic model / Data collection / Database references / Category: atom_site / citation / citation_author
Item: _atom_site.occupancy / _citation.country ..._atom_site.occupancy / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 2.1May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_struct_special_symmetry / pdbx_validate_symm_contact
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 2.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHONATE MONOESTER HYDROLASE
B: PHOSPHONATE MONOESTER HYDROLASE
C: PHOSPHONATE MONOESTER HYDROLASE


Theoretical massNumber of molelcules
Total (without water)180,6313
Polymers180,6313
Non-polymers00
Water15,331851
1
A: PHOSPHONATE MONOESTER HYDROLASE

A: PHOSPHONATE MONOESTER HYDROLASE

B: PHOSPHONATE MONOESTER HYDROLASE

B: PHOSPHONATE MONOESTER HYDROLASE


Theoretical massNumber of molelcules
Total (without water)240,8414
Polymers240,8414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
crystal symmetry operation6_554-x+1/2,-y+1/2,z-11
crystal symmetry operation1_554x,y,z-11
Buried area15840 Å2
ΔGint-61 kcal/mol
Surface area67240 Å2
MethodPISA
2
C: PHOSPHONATE MONOESTER HYDROLASE

C: PHOSPHONATE MONOESTER HYDROLASE

C: PHOSPHONATE MONOESTER HYDROLASE

C: PHOSPHONATE MONOESTER HYDROLASE


Theoretical massNumber of molelcules
Total (without water)240,8414
Polymers240,8414
Non-polymers00
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 area15940 Å2
ΔGint-46.4 kcal/mol
Surface area67210 Å2
MethodPISA
3
B: PHOSPHONATE MONOESTER HYDROLASE

B: PHOSPHONATE MONOESTER HYDROLASE

A: PHOSPHONATE MONOESTER HYDROLASE

A: PHOSPHONATE MONOESTER HYDROLASE


Theoretical massNumber of molelcules
Total (without water)240,8414
Polymers240,8414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
crystal symmetry operation6_556-x+1/2,-y+1/2,z+11
crystal symmetry operation1_556x,y,z+11
Buried area15840 Å2
ΔGint-61 kcal/mol
Surface area67240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)190.500, 274.620, 96.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-2116-

HOH

21A-2117-

HOH

31C-2085-

HOH

41C-2105-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.3334, 0.9428, 0.001135), (0.9428, -0.3334, -0.000943), (-0.000511, 0.001384, -1)-33.07, 46.71, 103.9
2given(-0.8184, -0.5746, -0.002245), (-0.5746, 0.8184, -0.00055), (0.002153, 0.00084, -1)204.5, 10.97, 51.72

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Components

#1: Protein PHOSPHONATE MONOESTER HYDROLASE


Mass: 60210.281 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RUEGERIA POMEROYI (bacteria) / Strain: DSS-3
Description: GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURE (DSMZ)
Plasmid: PASK-IBA5PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5LKJ1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 851 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL SEQUENCE MASWSHPQFEKGAETAVPNSSSVPGDPSS IS DERIVED FROM THE EXPRESSION VECTOR

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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: 3.49 Å3/Da / Density % sol: 64.8 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M BIS-TRIS-PROPANE PH 7.0, 9% (W/V) PEG 8000, 0.2 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.24→19.75 Å / Num. obs: 119850 / % possible obs: 99 % / Observed criterion σ(I): 1.5 / Redundancy: 14.2 % / Biso Wilson estimate: 28.78 Å2 / Rmerge(I) obs: 0.39 / Net I/σ(I): 6.6
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 9.8 % / Rmerge(I) obs: 1.47 / Mean I/σ(I) obs: 1.6 / % possible all: 90.6

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VQR
Resolution: 2.24→18.35 Å / Cor.coef. Fo:Fc: 0.8787 / Cor.coef. Fo:Fc free: 0.8416 / SU R Cruickshank DPI: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.194 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.169
RfactorNum. reflection% reflectionSelection details
Rfree0.2297 6018 5.03 %RANDOM
Rwork0.1963 ---
obs0.198 119744 99.03 %-
Displacement parametersBiso mean: 24.31 Å2
Baniso -1Baniso -2Baniso -3
1--7.0857 Å20 Å20 Å2
2---1.214 Å20 Å2
3---8.2997 Å2
Refine analyzeLuzzati coordinate error obs: 0.285 Å
Refinement stepCycle: LAST / Resolution: 2.24→18.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12030 0 0 851 12881
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112393HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0416923HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d4092SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes294HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1842HARMONIC5
X-RAY DIFFRACTIONt_it12393HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.88
X-RAY DIFFRACTIONt_other_torsion17.17
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1578SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14771SEMIHARMONIC4
LS refinement shellResolution: 2.24→2.3 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2429 381 4.74 %
Rwork0.2122 7649 -
all0.2136 8030 -
obs--99.03 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.32260.0799-0.24140.0691-0.25350.5926-0.017-0.0299-0.0464-0.0153-0.0266-0.02080.07660.01940.0436-0.0617-0.03460.0311-0.0232-0.0226-0.055867.075181.668426.4028
20.1920.01330.23560.21480.08570.5682-0.03550.02430.0328-0.05-0.00390.0190.03030.00870.0394-0.0733-0.04760.0222-0.0028-0.0273-0.068766.391682.650277.572
30.1050.0397-0.05670.12420.03280.732-0.0460.064-0.0013-0.0567-0.01130.0098-0.0326-0.09530.0573-0.03790.0031-0.0018-0.0328-0.0117-0.070571.7683136.80825.597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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