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- PDB-3rzz: Structure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant -

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Basic information

Entry
Database: PDB / ID: 3rzz
TitleStructure of Hydroxyethylphoshphonate Dioxygenase Y98F Mutant
ComponentsHydroxyethylphoshphonate Dioxygenase (PhpD)
KeywordsOXIDOREDUCTASE / NON HEME FE(II) DIOXYGENASE / CUPIN / BIOSYNTHETIC PROTEIN
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
: / 2-hydroxyethylphosphonate dioxygenase
Similarity search - Component
Biological speciesStreptomyces viridochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsCooke, H.A.
CitationJournal: Biochemistry / Year: 2011
Title: Mechanism and substrate recognition of 2-hydroxyethylphosphonate dioxygenase.
Authors: Peck, S.C. / Cooke, H.A. / Cicchillo, R.M. / Malova, P. / Hammerschmidt, F. / Nair, S.K. / van der Donk, W.A.
History
DepositionMay 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Sep 13, 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 / struct_ref_seq_dif / struct_site
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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hydroxyethylphoshphonate Dioxygenase (PhpD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,10116
Polymers48,4151
Non-polymers1,68615
Water4,864270
1
A: Hydroxyethylphoshphonate Dioxygenase (PhpD)
hetero molecules

A: Hydroxyethylphoshphonate Dioxygenase (PhpD)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,20232
Polymers96,8292
Non-polymers3,37230
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area15900 Å2
ΔGint-246 kcal/mol
Surface area33390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.747, 94.964, 101.396
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-501-

HOH

21A-666-

HOH

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Components

#1: Protein Hydroxyethylphoshphonate Dioxygenase (PhpD)


Mass: 48414.609 Da / Num. of mol.: 1 / Mutation: Y98F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces viridochromogenes (bacteria)
Strain: 1938 / Gene: phpD / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta 2(DE3) / References: UniProt: Q5IW40
#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.11 Å3/Da / Density % sol: 41.62 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 M sodium acetate, 0.1 M HEPES, 0.05 M cadmium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 18990 / % possible obs: 88.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rsym value: 0.046 / Net I/σ(I): 28.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 3 / Rsym value: 0.277 / % possible all: 62.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3G7D

3g7d


Resolution: 2.2→43 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1757 -Random
Rwork0.207 ---
all-21113 --
obs-17873 84.7 %-
Displacement parametersBiso mean: 16.7 Å2
Baniso -1Baniso -2Baniso -3
1--17.1 Å20 Å20 Å2
2--22.47 Å20 Å2
3----5.37 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3229 0 15 270 3514
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_mcbond_it1.26
X-RAY DIFFRACTIONc_scbond_it1.872
X-RAY DIFFRACTIONc_mcangle_it2.033
X-RAY DIFFRACTIONc_scangle_it2.7
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.022
RfactorNum. reflection% reflection
Rfree0.316 198 -
Rwork0.247 --
obs-1818 58.4 %

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