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- PDB-2bnm: The structure of Hydroxypropylphosphonic acid epoxidase from S. w... -

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Basic information

Entry
Database: PDB / ID: 2bnm
TitleThe structure of Hydroxypropylphosphonic acid epoxidase from S. wedmorenis.
ComponentsEPOXIDASE
KeywordsOXIDOREDUCTASE / EPOXIDASE / CUPIN / HTH / CATION-DEPENDANT / ZINC / FOSFOMYCIN
Function / homology
Function and homology information


(S)-2-hydroxypropylphosphonic acid epoxidase / phosphinothricin biosynthetic process / oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water / dioxygenase activity / antibiotic biosynthetic process / ferrous iron binding / protein homotetramerization / DNA-binding transcription factor activity / DNA binding / cytosol
Similarity search - Function
: / Cupin 2, conserved barrel / Cupin domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily ...: / Cupin 2, conserved barrel / Cupin domain / Helix-turn-helix / Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
(S)-2-hydroxypropylphosphonic acid epoxidase
Similarity search - Component
Biological speciesSTREPTOMYCES WEDMORENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1.7 Å
AuthorsMcLuskey, K. / Cameron, S. / Hunter, W.N.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure and Reactivity of Hydroxypropylphosphonic Acid Epoxidase in Fosfomycin Biosynthesis by a Cation- and Flavin-Dependent Mechanism.
Authors: Mcluskey, K. / Cameron, S. / Hammerschmidt, F. / Hunter, W.N.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Initiating a Crystallographic Analysis of Recombinant (S)-2-Hydroxypropylphosphonic Acid Epoxidase from Streptomyces Wedmorensis.
Authors: Cameron, S. / Mcluskey, K. / Chamberlayne, R. / Hallyburton, I. / Hunter, W.N.
History
DepositionMar 29, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 1, 2025Group: Advisory / Derived calculations
Category: database_PDB_caveat / pdbx_validate_close_contact ...database_PDB_caveat / pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EPOXIDASE
B: EPOXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,29419
Polymers42,7222
Non-polymers1,57217
Water9,854547
1
A: EPOXIDASE
B: EPOXIDASE
hetero molecules

A: EPOXIDASE
B: EPOXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,58838
Polymers85,4454
Non-polymers3,14434
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_675x-y+1,-y+2,-z1
Buried area19070 Å2
ΔGint-610.33 kcal/mol
Surface area33280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.363, 86.363, 221.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99993, 0.00565, -0.01069), (-0.00913, -0.9322, 0.36182), (-0.00792, 0.36189, 0.93219)
Vector: -4.21315, 145.03496, -26.932)

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Components

#1: Protein EPOXIDASE / HYDROXYPROPYLPHOSPHONIC ACID EPOXIDASE


Mass: 21361.127 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES WEDMORENSIS (bacteria) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q56185
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.27 Å3/Da / Density % sol: 45.36 %
Description: MODEL USED FOR RIGID BODY REFINEMENT HAS JUST BEEN DEPOSITED.
Crystal growpH: 7.5 / Details: 2.1 M AMMONIUM SULPHATE, 100 MM TRIS-HCL PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.27
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 53414 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Redundancy: 11.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 41.5
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.9 / % possible all: 82.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0003refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.7→30 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.055 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23 2716 5.1 %RANDOM
Rwork0.188 ---
obs0.191 50567 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20.2 Å20 Å2
2--0.41 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2944 0 77 547 3568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223252
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9754450
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2035389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43925.461152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31315564
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4661516
X-RAY DIFFRACTIONr_chiral_restr0.1050.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022393
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2190.21541
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.22204
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2443
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.2128
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.240
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.48442037
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.50883250
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.927101341
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.548101199
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: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.311 159
Rwork0.273 3004

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