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- PDB-5tk8: Structure of the HD-domain phosphohydrolase OxsA with Oxetanocin-... -

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Basic information

Entry
Database: PDB / ID: 5tk8
TitleStructure of the HD-domain phosphohydrolase OxsA with Oxetanocin-A monophosphate bound
ComponentsOxsA protein
KeywordsMETAL BINDING PROTEIN / metalloprotein
Function / homology
Function and homology information


5'-deoxynucleotidase YfbR-like / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-7D5 / OxsA protein
Similarity search - Component
Biological speciesBacillus megaterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsBridwell-Rabb, J. / Drennan, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32-GM108189 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: An HD domain phosphohydrolase active site tailored for oxetanocin-A biosynthesis.
Authors: Bridwell-Rabb, J. / Kang, G. / Zhong, A. / Liu, H.W. / Drennan, C.L.
History
DepositionOct 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Dec 14, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.pdbx_value_order / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OxsA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0653
Polymers22,7101
Non-polymers3562
Water2,072115
1
A: OxsA protein
hetero molecules

A: OxsA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1316
Polymers45,4202
Non-polymers7114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-11
Buried area5260 Å2
ΔGint-54 kcal/mol
Surface area17560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.031, 143.031, 53.786
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein OxsA protein


Mass: 22709.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus megaterium (bacteria) / Gene: oxsA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star (DE3) / References: UniProt: O24769
#2: Chemical ChemComp-7D5 / [(2S,3R,4R)-4-(6-amino-9H-purin-9-yl)-3-(hydroxymethyl)oxetan-2-yl]methyl dihydrogen phosphate / oxetanocin A monophosphate


Mass: 331.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O6P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M TRIS hydrochloride (pH 8.5), 0.2 M magnesium chloride hexahydrate, 30% w/v PEG 400 Protein solution contained: 50 mM HEPES (pH 8.0), 100 mM NaCl, and 5% v/v glycerol, and 5 mM OXT-P

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.64→41.29 Å / Num. obs: 25785 / % possible obs: 99.7 % / Redundancy: 17.3 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 55.8
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 3.1 / CC1/2: 0.886 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TK9

5tk9


Resolution: 1.64→41.289 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 1288 5.01 %
Rwork0.1794 --
obs0.1806 25696 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→41.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1576 0 23 115 1714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111668
X-RAY DIFFRACTIONf_angle_d1.2812257
X-RAY DIFFRACTIONf_dihedral_angle_d19.0041003
X-RAY DIFFRACTIONf_chiral_restr0.049251
X-RAY DIFFRACTIONf_plane_restr0.006287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.70570.31341390.25932634X-RAY DIFFRACTION98
1.7057-1.78330.24481430.22772712X-RAY DIFFRACTION100
1.7833-1.87730.24221440.20072731X-RAY DIFFRACTION100
1.8773-1.99490.21811420.19532696X-RAY DIFFRACTION100
1.9949-2.1490.21281420.18332715X-RAY DIFFRACTION100
2.149-2.36520.21171440.18762701X-RAY DIFFRACTION100
2.3652-2.70740.22151440.18082731X-RAY DIFFRACTION100
2.7074-3.41080.21711430.19042729X-RAY DIFFRACTION100
3.4108-41.30260.17921470.16252759X-RAY DIFFRACTION98

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