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- PDB-1xq6: X-ray Structure of Gene Product from Arabidopsis Thaliana At5g02240 -

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Basic information

Entry
Database: PDB / ID: 1xq6
TitleX-ray Structure of Gene Product from Arabidopsis Thaliana At5g02240
Componentsunknown protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PROTEIN STRUCTURE INITIATIVE / CESG / AT5G02240 / NADP / PSI / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


response to abscisic acid / apoplast / plant-type vacuole / chloroplast stroma / oxidoreductase activity / plasma membrane / cytosol
Similarity search - Function
Sanguinarine reductase SARED1-like / NAD(P)H-binding / NAD(P)-binding domain / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Uncharacterized protein At5g02240
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsWesenberg, G.E. / Smith, D.W. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be published
Title: X-ray Structure of Gene Product from Arabidopsis Thaliana At5g02240
Authors: Center for Eukaryotic Structural Genomics
History
DepositionOct 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: unknown protein
B: unknown protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6724
Polymers54,1862
Non-polymers1,4872
Water7,206400
1
A: unknown protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8362
Polymers27,0931
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: unknown protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8362
Polymers27,0931
Non-polymers7431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.750, 69.799, 83.828
Angle α, β, γ (deg.)90.00, 96.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein unknown protein


Mass: 27092.766 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At5g02240 / Plasmid: pVP-13 (pQE derivative) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) p(LacI+RARE) / References: UniProt: Q94EG6
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 400 / 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 (%)
12.5151
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop6.510 MG/ML PROTEIN, 28 PERCENT PEG 4K, 0.034 M SODIUM MALONATE, 0.10 M BISTRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, hanging drop6.510 MG/ML PROTEIN, 24 PERCENT PEG 4K, 0.136 M SODIUM MALONATE, 0.10 M BISTRIS, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 14-ID-B10.9793
SYNCHROTRONAPS 14-ID-B20.9794, 0.9790, 0.9637
Detector
TypeIDDetectorDateDetails
MAR CCD 165 mm1CCDAug 9, 2004bent cylindrical Si-mirror (Rh coating)
MAR CCD 165 mm2CCDAug 8, 2004bent cylindrical Si-mirror (Rh coating)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond (111) double-crystalSINGLE WAVELENGTHMx-ray1
2Diamond (111) double-crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97941
30.9791
40.96371
ReflectionResolution: 1.8→23.565 Å / Num. obs: 52253 / % possible obs: 93.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.043 / Χ2: 0.921 / Net I/σ(I): 19.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allΧ2% possible all
1.8-1.8650.6932.6748110.7887.3
1.86-1.940.51748990.93988.3
1.94-2.030.36349181.17989.3
2.03-2.130.21151041.20192
2.13-2.270.12653151.06395.6
2.27-2.440.08953580.99296.9
2.44-2.690.05754990.81998.6
2.69-3.080.04255220.82999.2
3.08-3.880.02755520.77799.3
3.88-1000.02152750.73992.6

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MADD res high: 2.05 Å / D res low: 20 Å / FOM : 0.46 / Reflection: 32618
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
1110.97951.3-10.73
1120.97924.28-8.04
1130.96413.31-3.89
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
17.55916.73313.481SE300.99
247.85413.98934.261SE50.31.03
319.01518.2435.408SE600.81
417.7714.99936.01SE600.74
Phasing MAD shell
Resolution (Å)FOM Reflection
7.15-200.711758
4.59-7.150.72859
3.61-4.590.723614
3.07-3.610.644184
2.72-3.070.544664
2.46-2.720.395065
2.27-2.460.255376
2.12-2.270.155098
Phasing dmFOM : 0.61 / FOM acentric: 0.6 / FOM centric: 0.64 / Reflection: 32619 / Reflection acentric: 29470 / Reflection centric: 3149
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.9-19.8810.960.960.915371149388
3.7-5.90.940.950.8846273954673
2.9-3.70.850.860.7857185100618
2.6-2.90.670.680.5556415147494
2.2-2.60.420.430.3597609082678
2.1-2.20.230.230.2253365038298

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMACrefmac_5.2.0005refinement
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.8→23.57 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.274 / WRfactor Rwork: 0.218 / SU B: 5.126 / SU ML: 0.154 / SU R Cruickshank DPI: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.16 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2776 2445 5.165 %RANDOM
Rwork0.2183 ---
all0.221 ---
obs0.221 47341 95.167 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 32.229 Å2
Baniso -1Baniso -2Baniso -3
1--1.807 Å20 Å20.272 Å2
2---0.278 Å20 Å2
3---2.141 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 96 400 4310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0223984
X-RAY DIFFRACTIONr_angle_refined_deg1.8332.0085402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0725504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.07725.57158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82515684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4541516
X-RAY DIFFRACTIONr_chiral_restr0.1320.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022940
X-RAY DIFFRACTIONr_nbd_refined0.2190.22037
X-RAY DIFFRACTIONr_nbtor_refined0.310.22742
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2350
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.216
X-RAY DIFFRACTIONr_mcbond_it1.80822585
X-RAY DIFFRACTIONr_mcangle_it2.86444008
X-RAY DIFFRACTIONr_scbond_it4.8161589
X-RAY DIFFRACTIONr_scangle_it6.38181394
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.8460.4141620.3613058360889.246
1.846-1.8970.4261700.3332976352689.223
1.897-1.9510.371780.3013012353290.317
1.951-2.0110.3381640.2642900331492.456
2.011-2.0760.3061490.2722897321594.743
2.076-2.1490.3121500.2492912318596.138
2.149-2.2290.3841540.2452836308996.795
2.229-2.3190.2961540.2432662290097.103
2.319-2.4210.2911380.2362610280797.898
2.421-2.5380.2861410.2372532270099
2.538-2.6740.2761380.2272393254299.567
2.674-2.8340.3191210.2212300243999.262
2.834-3.0260.2341090.2152154229498.649
3.026-3.2640.2891060.2042021213499.672
3.264-3.5690.2621040.1861860197399.544
3.569-3.9790.242850.1731672179797.774
3.979-4.5730.226660.1631461158996.098
4.573-5.5480.211700.1821253136097.279
5.548-7.6380.205620.214965108294.917
7.638-23.570.208240.2342265967.678

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