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- PDB-4yar: 2-Hydroxyethylphosphonate dioxygenase (HEPD) E176H -

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Basic information

Entry
Database: PDB / ID: 4yar
Title2-Hydroxyethylphosphonate dioxygenase (HEPD) E176H
Components2-hydroxyethylphosphonate dioxygenase
KeywordsOXIDOREDUCTASE / Dioxygenase
Function / homology
Function and homology information


2-hydroxyethylphosphonate dioxygenase / organic phosphonate biosynthetic process / phosphinothricin biosynthetic process / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / antibiotic biosynthetic process / ferrous iron binding / protein homodimerization activity / DNA binding / identical protein binding
Similarity search - Function
Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / 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 ...Helix-turn-helix XRE-family like proteins / lambda repressor-like DNA-binding domains / 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
ACETATE ION / : / 2-hydroxyethylphosphonate dioxygenase
Similarity search - Component
Biological speciesStreptomyces viridochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsChekan, J.R. / Nair, S.K.
CitationJournal: J.Am.Chem.Soc. / Year: 2015
Title: A Common Late-Stage Intermediate in Catalysis by 2-Hydroxyethyl-phosphonate Dioxygenase and Methylphosphonate Synthase.
Authors: Peck, S.C. / Chekan, J.R. / Ulrich, E.C. / Nair, S.K. / van der Donk, W.A.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Data collection
Revision 1.3Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Sep 27, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_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

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Assembly

Deposited unit
A: 2-hydroxyethylphosphonate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,42314
Polymers48,1571
Non-polymers1,26513
Water3,729207
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 2-hydroxyethylphosphonate dioxygenase
hetero molecules

A: 2-hydroxyethylphosphonate dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,84528
Polymers96,3152
Non-polymers2,53026
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area14980 Å2
ΔGint-186 kcal/mol
Surface area33910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.286, 95.953, 101.142
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-682-

HOH

21A-706-

HOH

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Components

#1: Protein 2-hydroxyethylphosphonate dioxygenase / / Hydroxyethylphosphonate dioxygenase / Phosphinothricin tripeptide biosynthesis protein D


Mass: 48157.375 Da / Num. of mol.: 1 / Mutation: E176H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces viridochromogenes (bacteria)
Gene: hepD, phpD, SSQG_01041 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5IW40, 2-hydroxyethylphosphonate dioxygenase
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: Cd
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / 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: 2.15 Å3/Da / Density % sol: 42.75 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 M sodium acetate, 0.1 M HEPES pH 7.5, 0.05 M cadmium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.75→63.75 Å / Num. obs: 40013 / % possible obs: 100 % / Redundancy: 14.1 % / Rsym value: 0.083 / Net I/σ(I): 21.4
Reflection shellResolution: 1.75→1.756 Å / Redundancy: 14.1 % / Mean I/σ(I) obs: 4 / Rsym value: 0.699 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3G7D

3g7d


Resolution: 1.75→63.75 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.939 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23789 2091 5 %RANDOM
Rwork0.19566 ---
obs0.19774 40013 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.444 Å2
Baniso -1Baniso -2Baniso -3
1--1.95 Å20 Å2-0 Å2
2--1.56 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 1.75→63.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3282 0 19 207 3508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193414
X-RAY DIFFRACTIONr_bond_other_d0.0020.023143
X-RAY DIFFRACTIONr_angle_refined_deg1.861.9464668
X-RAY DIFFRACTIONr_angle_other_deg0.93537208
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1915436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.83322.688160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.88315497
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8321533
X-RAY DIFFRACTIONr_chiral_restr0.1230.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213969
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02814
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_it2.7482.7591734
X-RAY DIFFRACTIONr_mcbond_other2.7422.7571731
X-RAY DIFFRACTIONr_mcangle_it4.1224.1292169
X-RAY DIFFRACTIONr_mcangle_other4.1214.132170
X-RAY DIFFRACTIONr_scbond_it3.5153.1021680
X-RAY DIFFRACTIONr_scbond_other3.5163.1021681
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3354.5262499
X-RAY DIFFRACTIONr_long_range_B_refined9.75323.2053951
X-RAY DIFFRACTIONr_long_range_B_other9.77923.1573907
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 145 -
Rwork0.232 2938 -
obs--100 %

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