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- PDB-3gbf: Phpd with cadmium complexed with hydroethylphosphonate (HEP) -

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Basic information

Entry
Database: PDB / ID: 3gbf
TitlePhpd with cadmium complexed with hydroethylphosphonate (HEP)
ComponentsPhpD
KeywordsBIOSYNTHETIC PROTEIN / Antibiotic biosynthesis / Iron dependent oxygenase
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-hydroxyethyl)phosphonic acid / : / 2-hydroxyethylphosphonate dioxygenase
Similarity search - Component
Biological speciesStreptomyces viridochromogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å
AuthorsZhang, H. / Nair, S.K.
CitationJournal: To be Published
Title: An Unusual Carbon-Carbon Bond Cleavage Reaction in the Biosynthesis of the Herbicide Phosphinothricin
Authors: Cicchillio, R.M. / Zhang, H. / Blodgett, J.A.V. / Whitteck, J.T. / Li, G. / Nair, S.K. / van der Donk, W.A. / Metcalf, W.W.
History
DepositionFeb 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 9, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PhpD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,97015
Polymers48,3831
Non-polymers1,58714
Water4,828268
1
A: PhpD
hetero molecules

A: PhpD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,94030
Polymers96,7662
Non-polymers3,17528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area15590 Å2
ΔGint-225 kcal/mol
Surface area32390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.974, 94.695, 101.595
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PhpD


Mass: 48382.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces viridochromogenes (bacteria)
Gene: phpD / Plasmid: pET-15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5IW40
#2: Chemical ChemComp-2HE / (2-hydroxyethyl)phosphonic acid


Mass: 126.048 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H7O4P
#3: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cd
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 268 / 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: 41.76 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1 M sodium acetate, 100 mM Hepes pH 7.5, 50 mM Cadmium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.92→50 Å / Num. obs: 31537 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Rsym value: 0.069 / Net I/σ(I): 28.6
Reflection shellResolution: 1.92→1.99 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 2916 / Rsym value: 0.29 / % possible all: 92.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.92→25 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.168 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25722 1587 5.1 %RANDOM
Rwork0.21172 ---
obs0.21398 29741 99.16 %-
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: 26.621 Å2
Baniso -1Baniso -2Baniso -3
1--2.48 Å20 Å20 Å2
2--3.55 Å20 Å2
3----1.07 Å2
Refinement stepCycle: LAST / Resolution: 1.92→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3165 0 20 268 3453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0213249
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.9494435
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2745411
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64822.759145
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.6215475
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1651529
X-RAY DIFFRACTIONr_chiral_restr0.0830.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022521
X-RAY DIFFRACTIONr_nbd_refined0.2090.21455
X-RAY DIFFRACTIONr_nbtor_refined0.2980.22217
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2263
X-RAY DIFFRACTIONr_metal_ion_refined0.2130.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.2133
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.237
X-RAY DIFFRACTIONr_mcbond_it0.711.52105
X-RAY DIFFRACTIONr_mcangle_it1.10323293
X-RAY DIFFRACTIONr_scbond_it1.84431302
X-RAY DIFFRACTIONr_scangle_it2.7184.51142
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 106 -
Rwork0.235 1958 -
obs--90.45 %

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