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- PDB-3egl: Crystal Structure of DegV Family Protein Cg2579 from Corynebacter... -

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Basic information

Entry
Database: PDB / ID: 3egl
TitleCrystal Structure of DegV Family Protein Cg2579 from Corynebacterium glutamicum
ComponentsDegV family protein
Keywordsstructural genomics / unknown function / alpha-beta-alpha sandwich / methylated lysines / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyDegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / : / lipid binding / FORMIC ACID / PALMITIC ACID / DegV domain-containing protein Cgl2349/cg2579
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.41 Å
AuthorsKim, Y. / Tesar, C. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of DegV Family Protein Cg2579 from Corynebacterium glutamicum
Authors: Kim, Y. / Tesar, C. / Abdullah, J. / Joachimiak, A.
History
DepositionSep 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description ...Advisory / Refinement description / Source and taxonomy / Version format compliance
Revision 1.2Mar 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_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_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: DegV family protein
B: DegV family protein
C: DegV family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,7247
Polymers89,9093
Non-polymers8154
Water8,251458
1
A: DegV family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2262
Polymers29,9701
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DegV family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2262
Polymers29,9701
Non-polymers2561
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DegV family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2723
Polymers29,9701
Non-polymers3022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.253, 151.667, 76.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein DegV family protein / UPF0230 protein Cgl2349/cg2579


Mass: 29969.598 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: N-term 6 HIs tag with TEV protease cut site / Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Strain: ATCC 13032 / Gene: Cgl2349, cg2579 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 / References: UniProt: Q8NN60
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C16H32O2
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 458 / 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: 3.38 Å3/Da / Density % sol: 63.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium formate, 20 % w/v Polyehtlyene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 9, 2008 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→49.3 Å / Num. all: 47822 / Num. obs: 47822 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.7 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.8
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.716 / Mean I/σ(I) obs: 2.5 / Num. unique all: 2367 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
Cootmodel building
REFMAC5.5.0053refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.41→49.3 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.136 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2420 5.1 %RANDOM
Rwork0.179 ---
all0.181 45350 --
obs0.181 45350 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.381 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2---0.02 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.41→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5935 0 54 458 6447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226175
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.9818376
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1035810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82523.775249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10415927
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0511552
X-RAY DIFFRACTIONr_chiral_restr0.0990.2979
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214570
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_it0.7921.54004
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.52526410
X-RAY DIFFRACTIONr_scbond_it2.68832171
X-RAY DIFFRACTIONr_scangle_it4.424.51966
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.408→2.471 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 167 -
Rwork0.231 3158 -
obs-3325 95.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9747-0.82350.3861.1983-0.33021.1799-0.0261-0.05020.0609-0.0229-0.0076-0.0022-0.0724-0.10550.03370.04360.01010.01460.0147-0.00760.016226.195627.594647.673
21.7866-0.936-0.09692.5231-0.16170.59930.0840.1722-0.0812-0.1381-0.05630.1877-0.0118-0.0799-0.02760.0472-0.0029-0.03370.0379-0.0070.041232.8723-9.066342.4338
31.49590.8132-0.10572.0985-0.22551.550.02620.0350.040.024-0.0797-0.00340.1126-0.10480.05350.05690.02750.0030.0493-0.0040.003614.368220.51978.7277
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 263
2X-RAY DIFFRACTION2B-2 - 264
3X-RAY DIFFRACTION3C0 - 264

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