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- PDB-4uph: Crystal Structure of Phosphonate Monoester Hydrolase of Agrobacte... -

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Basic information

Entry
Database: PDB / ID: 4uph
TitleCrystal Structure of Phosphonate Monoester Hydrolase of Agrobacterium radiobacter
ComponentsSULFATASE (SULFURIC ESTER HYDROLASE) PROTEIN
KeywordsHYDROLASE
Function / homology
Function and homology information


sulfuric ester hydrolase activity / metal ion binding
Similarity search - Function
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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Sulfatase (Sulfuric ester hydrolase) protein
Similarity search - Component
Biological speciesAGROBACTERIUM RADIOBACTER K84 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFischer, G. / Loo, B.v. / Hyvonen, M. / Hollfelder, F.
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 1.1Nov 16, 2016Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other
Revision 1.2Sep 13, 2017Group: Advisory / Data collection / Category: diffrn_detector / pdbx_validate_polymer_linkage / Item: _diffrn_detector.type
Revision 1.3Dec 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._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
Revision 2.0Jan 30, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Experimental preparation
Category: atom_site / exptl_crystal_grow ...atom_site / exptl_crystal_grow / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _struct_conn.ptnr1_label_atom_id
Revision 3.0Apr 24, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: diffrn_source / entity_poly ...diffrn_source / entity_poly / pdbx_seq_map_depositor_info / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can ..._diffrn_source.pdbx_synchrotron_site / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code / _struct_conn.pdbx_leaving_atom_flag
Revision 3.1May 8, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
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 3.2Jul 10, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SULFATASE (SULFURIC ESTER HYDROLASE) PROTEIN
B: SULFATASE (SULFURIC ESTER HYDROLASE) PROTEIN
C: SULFATASE (SULFURIC ESTER HYDROLASE) PROTEIN
D: SULFATASE (SULFURIC ESTER HYDROLASE) PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,05912
Polymers240,8204
Non-polymers2398
Water6,125340
1
A: SULFATASE (SULFURIC ESTER HYDROLASE) PROTEIN
C: SULFATASE (SULFURIC ESTER HYDROLASE) PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5306
Polymers120,4102
Non-polymers1204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-35.9 kcal/mol
Surface area35230 Å2
MethodPISA
2
B: SULFATASE (SULFURIC ESTER HYDROLASE) PROTEIN
D: SULFATASE (SULFURIC ESTER HYDROLASE) PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,5306
Polymers120,4102
Non-polymers1204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-37.8 kcal/mol
Surface area35350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)232.690, 232.690, 112.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
SULFATASE (SULFURIC ESTER HYDROLASE) PROTEIN / ARPMH


Mass: 60205.113 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: CYSTEIN 94 TO FORMYLGLYCINE POSTTRANSLATIONAL MODIFICATION
Source: (gene. exp.) AGROBACTERIUM RADIOBACTER K84 (bacteria)
Plasmid: PASK-IBA5PLUS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9JE48
#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 / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details3,3-DIHYDROXY L-ALANINE (DDZ): POSTTRANSLATIONAL MODIFICATION OF CYSTEIN TO FORMYLGLYCINE

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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: 3.15 Å3/Da / Density % sol: 61 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7 / Details: 0.1M TRIS-HCL PH=7.0 10% PEG 8000 0.2M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9788
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 2.5→58.17 Å / Num. obs: 106159 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / Biso Wilson estimate: 66.19 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.8
Reflection shellResolution: 2.5→2.8 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
AutoPROCdata reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→58.17 Å / Cor.coef. Fo:Fc: 0.9348 / Cor.coef. Fo:Fc free: 0.9181 / SU R Cruickshank DPI: 0.303 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.295 / SU Rfree Blow DPI: 0.214 / SU Rfree Cruickshank DPI: 0.219
RfactorNum. reflection% reflectionSelection details
Rfree0.2251 5295 4.99 %RANDOM
Rwork0.1959 ---
obs0.1974 106081 99.96 %-
Displacement parametersBiso mean: 59.65 Å2
Baniso -1Baniso -2Baniso -3
1-8.0763 Å20 Å20 Å2
2--8.0763 Å20 Å2
3----16.1525 Å2
Refinement stepCycle: LAST / Resolution: 2.5→58.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15704 0 8 340 16052
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0116180HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0522064HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5280SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes368HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2428HARMONIC5
X-RAY DIFFRACTIONt_it16180HARMONIC20
X-RAY DIFFRACTIONt_nbd3SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion17.86
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2008SEMIHARMONIC5
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_contact18730SEMIHARMONIC4
LS refinement shellResolution: 2.5→2.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2904 391 5.05 %
Rwork0.2417 7352 -
all0.2441 7743 -
obs--99.96 %

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