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- PDB-3fok: Crystal Structure of Cgl0159 From Corynebacterium glutamicum (Bre... -

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Basic information

Entry
Database: PDB / ID: 3fok
TitleCrystal Structure of Cgl0159 From Corynebacterium glutamicum (Brevibacterium flavum). Northeast Structural Genomics Target CgR115
Componentsuncharacterized protein Cgl0159
Keywordsstructural genomics / unknown function / Cgl0159 / Brevibacterium flavum. / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyCgl0159-like / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / Deoxyribose-phosphate aldolase
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsSeetharaman, J. / Neely, H. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. ...Seetharaman, J. / Neely, H. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of Cgl0159 From Corynebacterium glutamicum (Brevibacterium flavum). Northeast Structural Genomics Target CgR115
Authors: Seetharaman, J. / Neely, H. / Wang, H. / Janjua, H. / Foote, E.L. / Xiao, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionDec 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: uncharacterized protein Cgl0159
B: uncharacterized protein Cgl0159
C: uncharacterized protein Cgl0159
D: uncharacterized protein Cgl0159
E: uncharacterized protein Cgl0159
F: uncharacterized protein Cgl0159
G: uncharacterized protein Cgl0159
H: uncharacterized protein Cgl0159
I: uncharacterized protein Cgl0159
J: uncharacterized protein Cgl0159


Theoretical massNumber of molelcules
Total (without water)336,17910
Polymers336,17910
Non-polymers00
Water12,881715
1
A: uncharacterized protein Cgl0159
B: uncharacterized protein Cgl0159
F: uncharacterized protein Cgl0159
G: uncharacterized protein Cgl0159
H: uncharacterized protein Cgl0159


Theoretical massNumber of molelcules
Total (without water)168,0895
Polymers168,0895
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15480 Å2
ΔGint-78 kcal/mol
Surface area50430 Å2
MethodPISA
2
C: uncharacterized protein Cgl0159
D: uncharacterized protein Cgl0159
E: uncharacterized protein Cgl0159
I: uncharacterized protein Cgl0159
J: uncharacterized protein Cgl0159


Theoretical massNumber of molelcules
Total (without water)168,0895
Polymers168,0895
Non-polymers00
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15500 Å2
ΔGint-79 kcal/mol
Surface area50410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.000, 176.209, 104.239
Angle α, β, γ (deg.)90.00, 101.94, 90.00
Int Tables number4
Space group name H-MP1211
Detailspentamer

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Components

#1: Protein
uncharacterized protein Cgl0159


Mass: 33617.855 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: Cgl0159, cg0198 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NTZ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 715 / 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: 2.51 Å3/Da / Density % sol: 51.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.2M NH4CL, 10% PEG 3350, , pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 256002 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 27.5 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 11.2
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 10 / Num. unique all: 25191 / % possible all: 96.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→39 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 59317.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.254 10534 4.9 %RANDOM
Rwork0.225 ---
obs0.225 214704 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.0521 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.04 Å20 Å2-0.7 Å2
2---5.66 Å20 Å2
3---8.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22080 0 0 715 22795
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.83
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 1620 4.9 %
Rwork0.306 31200 -
obs--87 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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