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- PDB-1sdj: X-RAY STRUCTURE OF YDDE_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSO... -

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Basic information

Entry
Database: PDB / ID: 1sdj
TitleX-RAY STRUCTURE OF YDDE_ECOLI NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET ET25.
ComponentsHypothetical protein yddE
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Isomerases; Racemases and epimerases / biosynthetic process / isomerase activity / protein homodimerization activity / cytoplasm
Similarity search - Function
Phenazine biosynthesis PhzF protein / Phenazine biosynthesis-like protein / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
Uncharacterized isomerase YddE
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsKuzin, A.P. / Edstrom, W. / Skarina, T. / Korniyenko, Y. / Savchenko, A. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Structure and function of the phenazine biosynthetic protein PhzF from Pseudomonas fluorescens.
Authors: Blankenfeldt, W. / Kuzin, A.P. / Skarina, T. / Korniyenko, Y. / Tong, L. / Bayer, P. / Janning, P. / Thomashow, L.S. / Mavrodi, D.V.
History
DepositionFeb 13, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 24, 2004ID: 1P9V
Revision 1.0Feb 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / 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_database_related.db_name / _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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein yddE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5556
Polymers34,0751
Non-polymers4805
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.047, 130.659, 48.555
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 Hypothetical protein yddE / ORFB


Mass: 34074.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YDDE, B1464 / Plasmid: PET15 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P37757
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / 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: 2.91 Å3/Da / Density % sol: 57.73 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / PH range low: 5 / PH range high: 4.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMligand1reservoir
324-30 %(w/v)PEG40001reservoir
40.1 Msodium citrate1reservoirpH4.4-5.0
50.2 M1reservoirNH4OAc

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97929, 0.97970, 0.97702
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 11, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979291
20.97971
30.977021
ReflectionResolution: 2.3→20 Å / Num. all: 140762 / Num. obs: 32871 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.247 / Num. unique all: 2943 / Rsym value: 0.247 / % possible all: 85.6
Reflection
*PLUS
% possible obs: 89.5 %
Reflection shell
*PLUS
Highest resolution: 2.3 Å / % possible obs: 85.6 % / Redundancy: 27 % / Mean I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→19.87 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 591533.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1554 5.1 %RANDOM
Rwork0.218 ---
obs0.218 30515 89.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.7607 Å2 / ksol: 0.333235 e/Å3
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20 Å2
2--0.82 Å20 Å2
3----2.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2379 0 25 144 2548
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d1.01
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 196 4.7 %
Rwork0.271 3973 -
obs--73 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.01

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