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- PDB-7rty: Crystal Structure of PsfC from Pseudomonas syringae PB-5123 -

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Basic information

Entry
Database: PDB / ID: 7rty
TitleCrystal Structure of PsfC from Pseudomonas syringae PB-5123
ComponentsPsfC
KeywordsBIOSYNTHETIC PROTEIN / Fosfomycin biosynthesis / metalloenzyme / Fe
Function / homologyPHP-associated / Polymerase/histidinol phosphatase-like / Metal-dependent hydrolases / TIM Barrel / Alpha-Beta Barrel / metal ion binding / Alpha Beta / : / PHP domain-containing protein
Function and homology information
Biological speciesPseudomonas syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.963 Å
AuthorsOngpipattanakul, C. / Nair, S.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Biosynthesis of fosfomycin in pseudomonads reveals an unexpected enzymatic activity in the metallohydrolase superfamily.
Authors: Simon, M.A. / Ongpipattanakul, C. / Nair, S.K. / van der Donk, W.A.
History
DepositionAug 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PsfC
B: PsfC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,3416
Polymers54,1182
Non-polymers2234
Water2,180121
1
A: PsfC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1703
Polymers27,0591
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PsfC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1703
Polymers27,0591
Non-polymers1122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.831, 106.831, 83.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number80
Space group name H-MI41
Components on special symmetry positions
IDModelComponents
11A-671-

HOH

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Components

#1: Protein PsfC


Mass: 27058.795 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas syringae (bacteria) / Strain: PB-5123 / Production host: Escherichia coli (E. coli) / References: UniProt: I6QY72
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.72 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.17-0.20 M sodium fluoride, 18-20% PEG 3,350, 0.1 M bis-tris propane pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.12713 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 8, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12713 Å / Relative weight: 1
ReflectionResolution: 1.96→65.548 Å / Num. obs: 30430 / % possible obs: 91.2 % / Redundancy: 7.8 % / CC1/2: 0.997 / Rmerge(I) obs: 0.09 / Rrim(I) all: 0.096 / Net I/σ(I): 15.6
Reflection shellResolution: 1.963→1.97 Å / Redundancy: 6 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 2.3 / Num. unique obs: 233 / CC1/2: 0.752 / % possible all: 68.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.963→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.376 / SU ML: 0.152 / Cross valid method: THROUGHOUT / ESU R: 0.243 / ESU R Free: 0.195 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25691 1511 5 %RANDOM
Rwork0.21646 ---
obs0.21848 28900 91.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.328 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refinement stepCycle: 1 / Resolution: 1.963→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3786 0 4 121 3911
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0123876
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.921.6315250
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3855486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18621.589214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76215634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5011532
X-RAY DIFFRACTIONr_chiral_restr0.0740.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022942
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.9274.1661953
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.0116.2322436
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1614.4561923
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined5.78556.7455676
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: 1.963→2.014 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 79 -
Rwork0.279 1758 -
obs--75.1 %

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