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- PDB-2ze3: Crystal Structure of DFA0005 Complexed with alpha-Ketoglutarate: ... -

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Basic information

Entry
Database: PDB / ID: 2ze3
TitleCrystal Structure of DFA0005 Complexed with alpha-Ketoglutarate: A Novel Member of the ICL/PEPM Superfamily from Alkali-tolerant Deinococcus ficus
ComponentsDFA0005
KeywordsISOMERASE / Deinococcus ficus / organic waste left-over decomposition / alkaliphilic / ICL/PEPM superfamily / alpha-ketoglutarate ligand
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #510 / Phosphoenolpyruvate-binding domains / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / 2-OXOGLUTARIC ACID
Function and homology information
Biological speciesDeinococcus ficus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsLiao, C.J. / Chin, K.H. / Chou, S.H.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of DFA0005 complexed with alpha-ketoglutarate: a novel member of the ICL/PEPM superfamily from alkali-tolerant Deinococcus ficus
Authors: Liao, C.J. / Chin, K.H. / Lin, C.H. / Tsai, P.S. / Lyu, P.C. / Young, C.C. / Wang, A.H. / Chou, S.H.
History
DepositionDec 5, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: DFA0005
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4202
Polymers29,2741
Non-polymers1461
Water4,558253
1
A: DFA0005
hetero molecules

A: DFA0005
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,8404
Polymers58,5482
Non-polymers2922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area6250 Å2
ΔGint-47 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.840, 108.840, 114.118
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-366-

HOH

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Components

#1: Protein DFA0005


Mass: 29273.871 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus ficus (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 3.33 Å3/Da / Density % sol: 63.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 25, 2007
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 189632 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.059

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.65→18.85 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 223849.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 8686 9.6 %RANDOM
Rwork0.223 ---
obs0.223 90686 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.5821 Å2 / ksol: 0.399115 e/Å3
Displacement parametersBiso mean: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å20.19 Å20 Å2
2---2.1 Å20 Å2
3---4.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.65→18.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2061 0 10 253 2324
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.026
X-RAY DIFFRACTIONc_angle_deg2.6
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d5.73
X-RAY DIFFRACTIONc_mcbond_it0.941.5
X-RAY DIFFRACTIONc_mcangle_it1.442
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.253 1509 10 %
Rwork0.242 13545 -
obs--99.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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