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- PDB-5zdn: The complex structure of FomD with CDP -

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Basic information

Entry
Database: PDB / ID: 5zdn
TitleThe complex structure of FomD with CDP
ComponentsFomD
KeywordsHYDROLASE / metalloprotein
Function / homology
Function and homology information


Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / antibiotic biosynthetic process / hydrolase activity / metal ion binding
Similarity search - Function
: / Domain of unknown function DUF402 / FomD-like superfamily / Protein of unknown function (DUF402)
Similarity search - Domain/homology
CYTIDINE-5'-DIPHOSPHATE / Cytidylyl-2-hydroxypropylphosphonate hydrolase
Similarity search - Component
Biological speciesStreptomyces fradiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsSato, S. / Miyanaga, A. / Kudo, F. / Eguchi, T.
CitationJournal: Biochemistry / Year: 2018
Title: Biochemical and Structural Analysis of FomD That Catalyzes the Hydrolysis of Cytidylyl ( S)-2-Hydroxypropylphosphonate in Fosfomycin Biosynthesis.
Authors: Sato, S. / Miyanaga, A. / Kim, S.Y. / Kuzuyama, T. / Kudo, F. / Eguchi, T.
History
DepositionFeb 23, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_symmetry / _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.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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FomD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5887
Polymers23,9951
Non-polymers5926
Water1,31573
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-41 kcal/mol
Surface area9210 Å2
2
A: FomD
hetero molecules

A: FomD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,17614
Polymers47,9912
Non-polymers1,18512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area4960 Å2
ΔGint-100 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.165, 77.452, 96.566
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-305-

MG

21A-426-

HOH

31A-441-

HOH

41A-463-

HOH

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Components

#1: Protein FomD


Mass: 23995.363 Da / Num. of mol.: 1 / Mutation: L139F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces fradiae (bacteria) / Gene: fomD / Plasmid: pHis8 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: D2SNF7
#2: Chemical ChemComp-CDP / CYTIDINE-5'-DIPHOSPHATE


Mass: 403.176 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N3O11P2
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.19 Å3/Da / Density % sol: 43.79 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: Tris-HCl, magnesium chloride, PEG 8000, EtOH, CDP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 21, 2017
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 14166 / % possible obs: 99.8 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 16.4
Reflection shellResolution: 2.02→2.07 Å / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1015 / % possible all: 97.4

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EXM

3exm


Resolution: 2.02→48.28 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 9.75 / SU ML: 0.134 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.18 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 693 4.9 %RANDOM
Rwork0.1929 ---
obs0.19559 13449 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.413 Å2
Baniso -1Baniso -2Baniso -3
1-1.62 Å20 Å20 Å2
2---1 Å20 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 2.02→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1575 0 35 73 1683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191674
X-RAY DIFFRACTIONr_bond_other_d0.0010.021481
X-RAY DIFFRACTIONr_angle_refined_deg2.0441.9172293
X-RAY DIFFRACTIONr_angle_other_deg0.93733384
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9665193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.21421.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63315231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1241520
X-RAY DIFFRACTIONr_chiral_restr0.120.2227
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211904
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02451
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 2.02→2.072 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.433 45 -
Rwork0.332 967 -
obs--97.4 %
Refinement TLS params.Method: refined / Origin x: 17.183 Å / Origin y: 13.667 Å / Origin z: 33.74 Å
111213212223313233
T0.0402 Å2-0.0007 Å20.013 Å2-0.1661 Å20.0087 Å2--0.1543 Å2
L0.3314 °2-0.0924 °2-0.0044 °2-1.0957 °2-0.2459 °2--0.9664 °2
S-0.0184 Å °0.0598 Å °-0.0599 Å °0.1957 Å °-0.0195 Å °0.0896 Å °-0.113 Å °-0.0234 Å °0.0379 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 202
2X-RAY DIFFRACTION1A301 - 306

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