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- PDB-3ffm: The crystal structure of human Gadd45g -

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Basic information

Entry
Database: PDB / ID: 3ffm
TitleThe crystal structure of human Gadd45g
ComponentsGrowth arrest and DNA-damage-inducible protein GADD45 gamma
KeywordsCELL CYCLE / beta-turn-helix
Function / homology
Function and homology information


positive regulation of p38MAPK cascade / positive regulation of JNK cascade / positive regulation of cold-induced thermogenesis / cell differentiation / regulation of cell cycle / positive regulation of apoptotic process / apoptotic process / 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 protein GADD45 gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsZhang, W.Z. / Fu, S. / Zeng, Z.H. / Rao, Z.H.
CitationJournal: To be Published
Title: The crystal structure of human Gadd45g
Authors: Zhang, W.Z. / Fu, S. / Zeng, Z.H. / Rao, Z.H.
History
DepositionDec 4, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 protein GADD45 gamma


Theoretical massNumber of molelcules
Total (without water)17,9191
Polymers17,9191
Non-polymers00
Water1,22568
1
A: Growth arrest and DNA-damage-inducible protein GADD45 gamma

A: Growth arrest and DNA-damage-inducible protein GADD45 gamma


Theoretical massNumber of molelcules
Total (without water)35,8382
Polymers35,8382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_545-x,-y-1/2,z1
Buried area1590 Å2
ΔGint-14 kcal/mol
Surface area14580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.413, 126.413, 126.413
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-161-

HOH

Details2

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Components

#1: Protein Growth arrest and DNA-damage-inducible protein GADD45 gamma / Cytokine-responsive protein CR6 / DNA-damage-inducible transcript 2 / DDIT-2


Mass: 17919.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CR6, DDIT2, GADD45G / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95257
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
14.773.81
2
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 25% PEG 3350, 0.2M Nacl, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDCrystal-ID
11
22
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONBSRF 3W1A20.9803
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 1, 2007
MAR CCD 165 mm2CCDJul 26, 2007
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.98031
ReflectionResolution: 2.3→50 Å / Num. all: 15266 / Num. obs: 13290 / Redundancy: 10.6 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXSphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.3→39.98 Å / SU R Cruickshank DPI: 25.37 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2598 1314 8.6 %RANDOM
Rwork0.2331 ---
all-15266 --
obs-13290 87.1 %-
Solvent computationBsol: 75.395 Å2
Displacement parametersBiso max: 167.64 Å2 / Biso mean: 70.74 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1088 0 0 68 1156
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d1.122
LS refinement shellResolution: 2.29→2.32 Å / Total num. of bins used: 30
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water.param

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