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- PDB-4kbx: Crystal structure of the pyridoxal-5'-phosphate dependent protein... -

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Basic information

Entry
Database: PDB / ID: 4kbx
TitleCrystal structure of the pyridoxal-5'-phosphate dependent protein yhfx from escherichia coli
ComponentsUncharacterized protein YhfX
KeywordsUNKNOWN FUNCTION / D-SERINE DEHYDRATASE FOLD / protein YhfX
Function / homology
Function and homology information


Lyase, Ornithine Decarboxylase; Chain A, domain 1 - #30 / : / YhfX-like, C-terminal domain / Alanine racemase, N-terminal / Alanine racemase, N-terminal domain / Lyase, Ornithine Decarboxylase; Chain A, domain 1 / PLP-binding barrel / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein YhfX
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.599 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Xiang, D.F. / Raushel, F.M. / Almo, S.C.
CitationJournal: To be Published
Title: Crystal structure of the pyridoxal-5'-phosphate dependent protein yhfx from escherichia coli
Authors: Fedorov, A.A. / Fedorov, E.V. / Xiang, D.F. / Raushel, F.M. / Almo, S.C.
History
DepositionApr 24, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein YhfX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4176
Polymers43,0091
Non-polymers4085
Water4,143230
1
A: Uncharacterized protein YhfX
hetero molecules

A: Uncharacterized protein YhfX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,83412
Polymers86,0182
Non-polymers81610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area7680 Å2
ΔGint-82 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.920, 82.651, 149.460
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-601-

HOH

21A-660-

HOH

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Components

#1: Protein Uncharacterized protein YhfX


Mass: 43009.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: yhfX, b3381, JW3344 / Production host: Escherichia coli (E. coli) / References: UniProt: P45550
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.5M Lithium sulfate, 0.1M Hepes , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 18, 2013
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.599→33.46 Å / Num. all: 53931 / Num. obs: 53931 / % possible obs: 97.92 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.599→33.46 Å / SU ML: 0.13 / σ(F): 0 / σ(I): 0 / Phase error: 20.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1979 1681 3.12 %RANDOM
Rwork0.1726 ---
obs0.1734 53931 97.92 %-
all-53931 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.599→33.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3011 0 24 230 3265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063104
X-RAY DIFFRACTIONf_angle_d1.0734225
X-RAY DIFFRACTIONf_dihedral_angle_d14.0331132
X-RAY DIFFRACTIONf_chiral_restr0.071477
X-RAY DIFFRACTIONf_plane_restr0.004540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5989-1.6460.27221170.23034014X-RAY DIFFRACTION91
1.646-1.69910.22511410.21264275X-RAY DIFFRACTION97
1.6991-1.75980.2681450.19824286X-RAY DIFFRACTION97
1.7598-1.83030.22151260.18684292X-RAY DIFFRACTION98
1.8303-1.91350.18781620.16964292X-RAY DIFFRACTION98
1.9135-2.01440.19531410.16664282X-RAY DIFFRACTION98
2.0144-2.14060.20621360.16374351X-RAY DIFFRACTION98
2.1406-2.30590.20191350.16864419X-RAY DIFFRACTION99
2.3059-2.53780.24661420.17494414X-RAY DIFFRACTION100
2.5378-2.90490.22381490.1844445X-RAY DIFFRACTION100
2.9049-3.65910.19261090.16894546X-RAY DIFFRACTION100
3.6591-33.46730.15221780.15574634X-RAY DIFFRACTION100

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