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- PDB-2oby: Crystal structure of Human P53 inducible oxidoreductase (TP53I3,PIG3) -

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Basic information

Entry
Database: PDB / ID: 2oby
TitleCrystal structure of Human P53 inducible oxidoreductase (TP53I3,PIG3)
ComponentsPutative quinone oxidoreductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


NADPH:quinone reductase / NADPH:quinone reductase activity / NADP metabolic process / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain / quinone binding / NADPH binding / protein homodimerization activity / cytosol
Similarity search - Function
Quinone oxidoreductase PIG3 / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily ...Quinone oxidoreductase PIG3 / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Quinone oxidoreductase PIG3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsPorte, S. / Valencia, E. / Farres, J. / Fita, I. / Pike, A.C.W. / Shafqat, N. / Debreczeni, J. / Johansson, C. / Haroniti, A. / Gileadi, O. ...Porte, S. / Valencia, E. / Farres, J. / Fita, I. / Pike, A.C.W. / Shafqat, N. / Debreczeni, J. / Johansson, C. / Haroniti, A. / Gileadi, O. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. / von Delft, F. / Oppermann, U. / Pares, X.
CitationJournal: To be Published
Title: Crystal structure of human P53 inducible oxidoreductase (TP53I3, PIG3)
Authors: Porte, S. / Valencia, E. / Farres, J. / Fita, I. / Pike, A.C.W. / Shafqat, N. / Debreczeni, J. / Johansson, C. / Haroniti, A. / Gileadi, O. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / ...Authors: Porte, S. / Valencia, E. / Farres, J. / Fita, I. / Pike, A.C.W. / Shafqat, N. / Debreczeni, J. / Johansson, C. / Haroniti, A. / Gileadi, O. / Arrowsmith, C.H. / Edwards, A. / Weigelt, J. / Sundstrom, M. / von Delft, F. / Oppermann, U. / Pares, X.
History
DepositionDec 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jan 31, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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 / _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: Putative quinone oxidoreductase
B: Putative quinone oxidoreductase
C: Putative quinone oxidoreductase
D: Putative quinone oxidoreductase
E: Putative quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)184,12010
Polymers180,4035
Non-polymers3,7175
Water543
1
A: Putative quinone oxidoreductase
B: Putative quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6484
Polymers72,1612
Non-polymers1,4872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-30 kcal/mol
Surface area26060 Å2
MethodPISA
2
C: Putative quinone oxidoreductase
hetero molecules

C: Putative quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6484
Polymers72,1612
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
3
D: Putative quinone oxidoreductase
hetero molecules

D: Putative quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6484
Polymers72,1612
Non-polymers1,4872
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
4
E: Putative quinone oxidoreductase
hetero molecules

E: Putative quinone oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,6484
Polymers72,1612
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Unit cell
Length a, b, c (Å)68.354, 184.359, 318.047
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12A
22D
32E
42A
52D
62E
13A
23D
33E
14A
24B
34C
44D
54E

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETGLNGLNAA1 - 3327 - 338
211METMETGLNGLNBB1 - 3327 - 338
311METMETGLNGLNCC1 - 3327 - 338
112METMETPROPROAA1 - 1227 - 128
212METMETPROPRODD1 - 1227 - 128
312METMETPROPROEE1 - 1227 - 128
422ARGARGGLNGLNAA296 - 332302 - 338
522ARGARGGLNGLNDD296 - 332302 - 338
622ARGARGGLNGLNEE296 - 332302 - 338
113GLUGLUGLNGLNAA123 - 295129 - 301
213GLUGLUGLNGLNDD123 - 295129 - 301
313GLUGLUGLNGLNEE123 - 295129 - 301
114NAPNAPNAPNAPAF1400
214NAPNAPNAPNAPBG1401
314NAPNAPNAPNAPCH1402
414NAPNAPNAPNAPDI1403
514NAPNAPNAPNAPEJ1404

NCS ensembles :
ID
1
2
3
4
DetailsThe biological assembly is a dimer. A and B dimerize in the asymmetric unit.

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Components

#1: Protein
Putative quinone oxidoreductase / Tumor protein p53- inducible protein 3 / p53-induced protein 3


Mass: 36080.605 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53I3, PIG3 / Plasmid: pGEX-4T-2 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q53FA7, Oxidoreductases
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30 % PEG 4000, 0.1 M Tris, 0.2 M sodium acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jun 10, 2005 / Details: Mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→19.94 Å / Num. all: 36209 / Num. obs: 36209 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 45.6 Å2
Reflection shellResolution: 3→3.2 Å / % possible all: 62.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345345DTBdata collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J8Z

2j8z


Resolution: 3→19.94 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.866 / SU B: 54.452 / SU ML: 0.418 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.505 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25968 1795 5 %RANDOM
Rwork0.21955 ---
all0.22155 34254 --
obs0.22155 34254 88.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--0.57 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 3→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12580 0 240 3 12823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.02213110
X-RAY DIFFRACTIONr_bond_other_d0.0040.028765
X-RAY DIFFRACTIONr_angle_refined_deg0.9352.01117835
X-RAY DIFFRACTIONr_angle_other_deg0.783321595
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.16951665
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83825.152495
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.798152170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7411545
X-RAY DIFFRACTIONr_chiral_restr0.0490.21995
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0214440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022335
X-RAY DIFFRACTIONr_nbd_refined0.1830.22668
X-RAY DIFFRACTIONr_nbd_other0.1620.28881
X-RAY DIFFRACTIONr_nbtor_refined0.1660.26285
X-RAY DIFFRACTIONr_nbtor_other0.080.26819
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2250
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1430.237
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1520.299
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.0691.510675
X-RAY DIFFRACTIONr_mcbond_other0.0161.53425
X-RAY DIFFRACTIONr_mcangle_it0.091213170
X-RAY DIFFRACTIONr_scbond_it0.16435696
X-RAY DIFFRACTIONr_scangle_it0.2514.54665
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A4223medium positional0.20.5
12B4223medium positional0.240.5
13C4223medium positional0.230.5
21A2005medium positional0.280.5
22D2005medium positional0.210.5
23E2005medium positional0.230.5
31A2218medium positional0.220.5
32D2218medium positional0.180.5
33E2218medium positional0.180.5
44A68medium positional0.180.5
44B68medium positional0.190.5
44C68medium positional0.150.5
44D68medium positional0.170.5
44E68medium positional0.170.5
11A4223medium thermal0.082
12B4223medium thermal0.072
13C4223medium thermal0.082
21A2005medium thermal0.072
22D2005medium thermal0.062
23E2005medium thermal0.062
31A2218medium thermal0.082
32D2218medium thermal0.072
33E2218medium thermal0.062
44A68medium thermal0.152
44B68medium thermal0.092
44C68medium thermal0.112
44D68medium thermal0.152
44E68medium thermal0.122
LS refinement shellResolution: 3.002→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.452 37 -
Rwork0.418 766 -
obs--27.48 %
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)
12.17891.6135-1.04732.5866-1.1431.84060.02270.12320.1379-0.22930.08910.0852-0.0685-0.128-0.1118-0.1732-0.06220.0313-0.14660.1403-0.128327.571639.1759-35.0355
22.5360.9265-0.4522.4114-1.33372.08050.0721-0.24650.27680.21950.09060.0289-0.1409-0.3148-0.1627-0.3006-0.0213-0.02570.07480.15640.0771-2.711231.7816-6.2786
30.78950.56730.27712.18841.41792.8555-0.13280.1533-0.0868-0.08660.0619-0.01820.26730.17950.0709-0.2318-0.01510.0762-0.18910.13-0.299129.0728-4.912-20.6592
41.1882-0.1133-0.70811.03040.84244.92290.0449-0.0174-0.2528-0.09530.001-0.01590.1599-0.1831-0.0459-0.138-0.05440.0665-0.20650.1106-0.0065-12.833938.8716-62.8347
51.96750.5842-1.63591.6355-0.91363.12140.0292-0.1709-0.0316-0.1734-0.02850.0497-0.0060.0922-0.00080.0737-0.04440.0185-0.22010.0089-0.289229.8354-5.2336-59.029
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 332
2X-RAY DIFFRACTION2B1 - 332
3X-RAY DIFFRACTION3C1 - 332
4X-RAY DIFFRACTION4D1 - 332
5X-RAY DIFFRACTION5E1 - 332

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