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- PDB-2wal: Crystal Structure of human GADD45gamma -

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Basic information

Entry
Database: PDB / ID: 2wal
TitleCrystal Structure of human GADD45gamma
ComponentsGROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 GAMMA
KeywordsAPOPTOSIS / CELL-CYCLE ARREST / DEVELOPMENTAL PROTEIN / GADD / DNA DAMAGE / G2/M PHASE / CDC2/CYCLINB1 / DIFFERENTIATION
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
MALONIC ACID / Growth arrest and DNA damage-inducible protein GADD45 gamma
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsBhattacharya, S. / Mueller, J.J. / Roske, Y. / Turnbull, A.P. / Quedenau, C. / Goetz, F. / Buessow, K. / Heinemann, U.
CitationJournal: To be Published
Title: The Crystal Structure of Human Gadd45Gamma
Authors: Bhattacharya, S. / Mueller, J.J. / Roske, Y. / Turnbull, A.P. / Quedenau, C. / Gotz, F. / Bussow, K. / Heinemann, U.
History
DepositionFeb 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 22, 2015Group: Non-polymer description
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 GAMMA
B: GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4164
Polymers34,2082
Non-polymers2082
Water97354
1
A: GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 GAMMA
B: GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 GAMMA
hetero molecules

A: GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 GAMMA
B: GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 GAMMA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,8338
Polymers68,4174
Non-polymers4164
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area10110 Å2
ΔGint-70.9 kcal/mol
Surface area30560 Å2
MethodPQS
Unit cell
Length a, b, c (Å)108.717, 108.717, 73.371
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein GROWTH ARREST AND DNA-DAMAGE-INDUCIBLE PROTEIN GADD45 GAMMA / GROWTH ARREST AND DNA DAMAGE PROTEIN 45 GAMMA / CYTOKINE-RESPONSIVE PROTEIN CR6 / DNA-DAMAGE- ...GROWTH ARREST AND DNA DAMAGE PROTEIN 45 GAMMA / CYTOKINE-RESPONSIVE PROTEIN CR6 / DNA-DAMAGE-INDUCIBLE TRANSCRIPT 2 / DDIT-2


Mass: 17104.148 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PQTEV / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O95257
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 58 TO ALA ENGINEERED RESIDUE IN CHAIN B, THR 58 TO ALA

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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: 3.69 Å3/Da / Density % sol: 66.4 % / Description: NONE
Crystal growpH: 5.5 / Details: 2 M MALONATE, 0.1 M BENZONATE, PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.90832
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2005 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.90832 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 21647 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 7.09 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 18.7
Reflection shellResolution: 2.3→20 Å / % possible all: 80.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.4→19.81 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.925 / SU B: 14.972 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.247 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N-TERMINAL 10 RESIDUES HAVE NO ELECTRON DENSITY IN BOTH MOLECULE A AND B. RESIDUES 105-118 AND RESIDUES 123-132 ARE NOT VISIBLE IN THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. N-TERMINAL 10 RESIDUES HAVE NO ELECTRON DENSITY IN BOTH MOLECULE A AND B. RESIDUES 105-118 AND RESIDUES 123-132 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP OF MOLECULE B AND ARE DISORDERED IN MOLECULE A.
RfactorNum. reflection% reflectionSelection details
Rfree0.251 988 5 %RANDOM
Rwork0.215 ---
obs0.216 18783 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20.48 Å20 Å2
2--0.95 Å20 Å2
3----1.43 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2142 0 14 54 2210
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222186
X-RAY DIFFRACTIONr_bond_other_d0.0010.021408
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.9682970
X-RAY DIFFRACTIONr_angle_other_deg0.90633464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.975281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.82325.91898
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.65615355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.2751510
X-RAY DIFFRACTIONr_chiral_restr0.0750.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022465
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02389
X-RAY DIFFRACTIONr_nbd_refined0.2330.2556
X-RAY DIFFRACTIONr_nbd_other0.1940.21490
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21101
X-RAY DIFFRACTIONr_nbtor_other0.0870.21207
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.220
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.23621821
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.94832263
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.7274.5856
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.2196707
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.53 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.345 142 -
Rwork0.27 2702 -
obs--100 %
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)
12.9564-0.23530.08954.6824-0.48552.698-0.1208-0.17040.30070.0789-0.0054-0.3686-0.0670.25740.12620.17410.09280.01980.0969-0.00430.0562-41.4933-19.163214.3657
242.04568.9445-23.796812.8692-17.707128.04842.4933-2.0175-2.32931.2176-3.4367-0.4446-0.9757-0.56170.94340.47720.3092-0.09190.8933-0.22250.9657-56.1558-22.404123.0432
311.7813-6.05660.608710.75010.3888.8053-0.2033-1.5465-1.54040.98680.4118-0.8171.74340.9161-0.20850.42980.1942-0.06360.23790.14470.2735-35.0275-26.592521.5331
45.0491.31930.166811.2391-4.84486.2258-0.31960.2476-0.4285-0.30940.0262-0.71640.34970.8210.29340.29260.15760.18250.2576-0.05010.1262-36.3617-24.53154.94
513.02210.21641.19823.2428-2.045811.0888-0.71172.15570.9897-2.8170.6083-0.6236-0.49040.72910.10340.574-0.33070.19210.78330.1105-0.2828-43.1152-14.1538-14.3937
60.0631-0.3763-0.47017.61820.04654.9194-0.46270.23590.7631-0.54560.3694-0.0699-0.38410.25130.09330.4112-0.1123-0.03350.12640.09790.3126-44.3826-3.0509-1.0956
748.766737.116933.939229.697828.910830.1698-1.2041.02921.9954-2.0492-0.8857-0.13710.60071.41182.08971.0134-0.63760.27421.49470.50760.7692-33.6657-6.8127-12.9916
824.548-0.720711.79459.97656.477413.46710.67422.2981.6155-1.3003-0.44270.3572-1.5220.7587-0.23150.6102-0.15030.06450.25630.44870.2091-44.6634-1.7276-8.9202
911.98342.76580.54172.8621-0.07298.5295-0.63261.48930.8071-0.850.58630.13860.01750.23810.04630.4282-0.1469-0.01580.24670.14590.0379-49.7554-15.8891-8.3279
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 104
2X-RAY DIFFRACTION2A105 - 115
3X-RAY DIFFRACTION3A116 - 131
4X-RAY DIFFRACTION4A132 - 158
5X-RAY DIFFRACTION5B11 - 38
6X-RAY DIFFRACTION6B39 - 96
7X-RAY DIFFRACTION7B97 - 107
8X-RAY DIFFRACTION8B117 - 123
9X-RAY DIFFRACTION9B130 - 158

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