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- PDB-5zdm: The ligand-free structure of FomD -

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Basic information

Entry
Database: PDB / ID: 5zdm
TitleThe ligand-free structure of FomD
ComponentsFomD
KeywordsHYDROLASE / metalloprotein
Function / homologyDomain of unknown function DUF402 / FomD-like superfamily / Protein of unknown function (DUF402) / FomD
Function and homology information
Biological speciesStreptomyces fradiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 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_label_seq_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_label_seq_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.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_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)24,3526
Polymers23,9951
Non-polymers3565
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area800 Å2
ΔGint-18 kcal/mol
Surface area10170 Å2
Unit cell
Length a, b, c (Å)40.474, 46.215, 52.504
Angle α, β, γ (deg.)90.00, 110.27, 90.00
Int Tables number4
Space group name H-MP1211

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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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 1.92 Å3/Da / Density % sol: 35.93 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Tris-HCl, calcium chloride, PEG 8000, trimethylamine N-oxide, cytosine

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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: Dec 22, 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: 1.38→50 Å / Num. obs: 36195 / % possible obs: 96.4 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 18
Reflection shellResolution: 1.38→1.41 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1840 / % possible all: 94.3

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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: 1.38→49.25 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.97 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.064 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19178 1756 4.9 %RANDOM
Rwork0.1635 ---
obs0.16486 34427 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.711 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å2-0 Å20.42 Å2
2---1.38 Å20 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.38→49.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1619 0 20 210 1849
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0191724
X-RAY DIFFRACTIONr_bond_other_d0.0020.021535
X-RAY DIFFRACTIONr_angle_refined_deg2.3841.9042354
X-RAY DIFFRACTIONr_angle_other_deg1.02833512
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5895203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.75122.10595
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.46915244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2761521
X-RAY DIFFRACTIONr_chiral_restr0.140.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0160.0211986
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02461
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: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.249 125 -
Rwork0.249 2512 -
obs--95.47 %
Refinement TLS params.Method: refined / Origin x: 8.848 Å / Origin y: -0.599 Å / Origin z: 9.216 Å
111213212223313233
T0.0527 Å20.0041 Å20.0058 Å2-0.1219 Å2-0.0083 Å2--0.0038 Å2
L0.3163 °2-0.2193 °2-0.1859 °2-0.5846 °20.0466 °2--0.6243 °2
S0.0257 Å °0.0136 Å °-0.0065 Å °-0.0428 Å °-0.0578 Å °0.0256 Å °0.0349 Å °-0.0459 Å °0.0321 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A10 - 207
2X-RAY DIFFRACTION1A301 - 305

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