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- PDB-3cg6: Crystal structure of Gadd45 gamma -

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Basic information

Entry
Database: PDB / ID: 3cg6
TitleCrystal structure of Gadd45 gamma
ComponentsGrowth arrest and DNA-damage-inducible 45 gamma
KeywordsCELL CYCLE / alpha/beta
Function / homology
Function and homology information


: / type II interferon production / : / T-helper 1 cell differentiation / positive regulation of p38MAPK cascade / positive regulation of JNK cascade / negative regulation of protein kinase activity / positive regulation of cold-induced thermogenesis / regulation of cell cycle / positive regulation of apoptotic process ...: / type II interferon production / : / T-helper 1 cell differentiation / positive regulation of p38MAPK cascade / positive regulation of JNK cascade / negative regulation of protein kinase activity / positive regulation of cold-induced thermogenesis / regulation of cell cycle / positive regulation of apoptotic process / apoptotic process / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Growth arrest and DNA damage-inducible protein GADD45 / Ribosomal protein L30/S12 / 60s Ribosomal Protein L30; Chain: A; / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Growth arrest and DNA-damage-inducible 45 gamma / Growth arrest and DNA damage-inducible protein GADD45 gamma
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSchrag, J.D. / Jiralerspong, S. / Banville, M. / Jaramillo, M.L. / O'Connor-McCourt, M.D.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: The crystal structure and dimerization interface of GADD45gamma.
Authors: Schrag, J.D. / Jiralerspong, S. / Banville, M. / Jaramillo, M.L. / O'Connor-McCourt, M.D.
History
DepositionMar 5, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Growth arrest and DNA-damage-inducible 45 gamma
B: Growth arrest and DNA-damage-inducible 45 gamma


Theoretical massNumber of molelcules
Total (without water)31,6012
Polymers31,6012
Non-polymers00
Water4,197233
1
A: Growth arrest and DNA-damage-inducible 45 gamma

B: Growth arrest and DNA-damage-inducible 45 gamma


Theoretical massNumber of molelcules
Total (without water)31,6012
Polymers31,6012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
2
A: Growth arrest and DNA-damage-inducible 45 gamma

A: Growth arrest and DNA-damage-inducible 45 gamma

B: Growth arrest and DNA-damage-inducible 45 gamma

B: Growth arrest and DNA-damage-inducible 45 gamma


Theoretical massNumber of molelcules
Total (without water)63,2024
Polymers63,2024
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
crystal symmetry operation2_655-x+1,-y,z+1/21
crystal symmetry operation4_555x,-y,-z1
Buried area6710 Å2
ΔGint-41.2 kcal/mol
Surface area22220 Å2
MethodPISA
3
A: Growth arrest and DNA-damage-inducible 45 gamma

A: Growth arrest and DNA-damage-inducible 45 gamma


Theoretical massNumber of molelcules
Total (without water)31,6012
Polymers31,6012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area2550 Å2
ΔGint-8.8 kcal/mol
Surface area12110 Å2
MethodPISA
4
B: Growth arrest and DNA-damage-inducible 45 gamma

B: Growth arrest and DNA-damage-inducible 45 gamma


Theoretical massNumber of molelcules
Total (without water)31,6012
Polymers31,6012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area1980 Å2
ΔGint-11.4 kcal/mol
Surface area12300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.024, 122.468, 105.421
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-160-

HOH

21A-224-

HOH

31B-160-

HOH

41B-202-

HOH

Noncrystallographic symmetry (NCS)NCS domain: (Details: A) / NCS domain segments: (Refine code: 6 )

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Components

#1: Protein Growth arrest and DNA-damage-inducible 45 gamma


Mass: 15800.597 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gadd45g / Plasmid: pGEX derivative / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99M58, UniProt: Q9Z111*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM HEPES, 1.9 M NaH2PO4 , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.4 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2005 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4 Å / Relative weight: 1
ReflectionResolution: 1.7→35.1 Å / Num. all: 31130 / Num. obs: 30674 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.74 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 15.7
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.73 % / Rmerge(I) obs: 0.269 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3063 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data collection
CrystalCleardata reduction
CrystalCleardata scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→35.1 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.959 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.131 / ESU R Free: 0.132 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27169 1547 5 %RANDOM
Rwork0.2238 ---
obs0.22617 29092 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.913 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---0.09 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.7→35.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2035 0 0 235 2270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222070
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.451.9632817
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5325265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.94925.6797
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.17915349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.31510
X-RAY DIFFRACTIONr_chiral_restr0.0990.2332
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021568
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.21077
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.21449
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2168
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.294
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1850.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9751.51358
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55422134
X-RAY DIFFRACTIONr_scbond_it2.3793788
X-RAY DIFFRACTIONr_scangle_it3.5414.5683
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 934 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.595
loose thermal1.6810
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 103 -
Rwork0.353 2174 -
obs--99.96 %

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