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- PDB-1ydw: X-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT4G09670 -

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Basic information

Entry
Database: PDB / ID: 1ydw
TitleX-RAY STRUCTURE OF GENE PRODUCT FROM ARABIDOPSIS THALIANA AT4G09670
ComponentsAX110P-like protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PROTEIN STRUCTURE INITIATIVE / PSI / Center for Eukaryotic Structural Genomics / CESG / AT4G09670
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / nucleotide binding / cytosol
Similarity search - Function
: / GFO/IDH/MocA C-terminal domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich ...: / GFO/IDH/MocA C-terminal domain / Gfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized oxidoreductase At4g09670
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.488 Å
AuthorsWesenberg, G.E. / 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 AT4G09670
Authors: Center for Eukaryotic Structural Genomics (CESG)
History
DepositionDec 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AX110P-like protein
B: AX110P-like protein


Theoretical massNumber of molelcules
Total (without water)79,6872
Polymers79,6872
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-31 kcal/mol
Surface area26930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.197, 107.663, 129.748
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AX110P-like protein


Mass: 39843.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g09670 / Plasmid: PVP-17 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q9SZ83
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.55 Å3/Da / Density % sol: 51.75 %
Description: UNMODELED DENSITY APPEARS IN BOTH SUBUNITS IN THE REGION BETWEEN LYS 43 TYR 63 PROBABLY DUE TO NADP.
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 MG/ML PROTEIN, 15% PEG4K, 0.168 M SODIUM CHLORIDE, 0.050 M PIPES, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.97927 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 24, 2004 / Details: BENT CYLINDRICAL SI-MIRROR (RH COATING)
RadiationMonochromator: Diamond (111) double-crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 2.488→33.749 Å / Num. obs: 29008 / % possible obs: 98.3 % / Redundancy: 13.4 % / Rmerge(I) obs: 0.107 / Χ2: 0.999 / Net I/σ(I): 13.245
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allΧ2% possible all
2.488-2.598.60.2984.32124390.66384.5
2.59-2.690.26328690.7698.8
2.69-2.820.24328920.7999.7
2.82-2.960.19629160.91699.9
2.96-3.150.16129011.039100
3.15-3.390.12929521.096100
3.39-3.730.11129361.051100
3.73-4.270.08829571.131100
4.27-5.380.0830021.109100
5.38-500.07731441.15799.4

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2.49 Å / D res low: 33.75 Å / FOM : 0.3 / Reflection: 26731
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
157.03920.02124.613SE41.20.76
231.9192.0946.748SE27.40.72
33.20717.87121.74SE33.50.73
427.40289.9754.131SE450.87
57.96316.19919.745SE38.40.63
63.40573.40529.672SE43.10.64
736.71393.7468.602SE18.60.42
854.36572.3726.491SE27.50.44
925.532101.51419.503SE38.90.49
1051.9590.78522.237SE40.70.45
1123.0332.1764.792SE48.80.54
1254.51410.0098.281SE53.80.54
Phasing MAD shell
Resolution (Å)FOM Reflection
8.89-33.750.391424
5.63-8.890.432431
4.41-5.630.393086
3.75-4.410.353580
3.31-3.750.323966
3-3.310.274200
2.76-30.214232
2.57-2.760.163812
Phasing dmFOM : 0.65 / FOM acentric: 0.66 / FOM centric: 0.64 / Reflection: 26733 / Reflection acentric: 23805 / Reflection centric: 2928
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.1-29.7340.920.920.771298939359
4.4-7.10.860.890.7339623318644
3.6-4.40.840.860.7448804282598
3.1-3.60.720.730.6547704305465
2.7-3.10.510.510.4678477235612
2.5-2.70.350.350.3739763726250

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.06phasing
RESOLVE2.06phasing
REFMACrefmac_5.2.0005refinement
RefinementMethod to determine structure: SAD / Resolution: 2.488→31.06 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.873 / WRfactor Rfree: 0.283 / WRfactor Rwork: 0.218 / SU B: 10.133 / SU ML: 0.229 / SU R Cruickshank DPI: 0.552 / Cross valid method: THROUGHOUT / ESU R: 0.552 / ESU R Free: 0.321 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SELENIUM C COEFFICIENT FOR STRUCTURE FACTOR CALCULATION SET TO -9.0000, MOLPROBITY USED TO ASSIST IN FINAL MODEL BUILDING
RfactorNum. reflection% reflectionSelection details
Rfree0.28254 1472 5.1 %RANDOM
Rwork0.21822 ---
all0.22155 ---
obs-27390 98.351 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.072 Å2
Baniso -1Baniso -2Baniso -3
1-1.389 Å20 Å20 Å2
2--2.068 Å20 Å2
3----3.457 Å2
Refinement stepCycle: LAST / Resolution: 2.488→31.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5340 0 0 123 5463
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0225453
X-RAY DIFFRACTIONr_angle_refined_deg2.051.9547408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0415689
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.31824.554224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.9315919
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0431525
X-RAY DIFFRACTIONr_chiral_restr0.1620.2854
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024061
X-RAY DIFFRACTIONr_nbd_refined0.2770.22846
X-RAY DIFFRACTIONr_nbtor_refined0.3260.23753
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2160.2289
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2380.214
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.340.23
X-RAY DIFFRACTIONr_mcbond_it1.75723550
X-RAY DIFFRACTIONr_mcangle_it3.21645566
X-RAY DIFFRACTIONr_scbond_it5.82662195
X-RAY DIFFRACTIONr_scangle_it7.87881842
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 (%)
2.488-2.5530.374860.2851651212781.664
2.553-2.6220.4071010.2551915207597.157
2.622-2.6970.327950.2441889200399.051
2.697-2.780.3521060.2661870197999.848
2.78-2.870.3241000.2441772187399.947
2.87-2.970.317870.2331756184599.892
2.97-3.0810.303840.22617061790100
3.081-3.2060.314870.21716201707100
3.206-3.3470.245760.21515721648100
3.347-3.5080.259810.20915121593100
3.508-3.6950.265760.21314351511100
3.695-3.9160.252790.20213531432100
3.916-4.1810.226950.19112711366100
4.181-4.5090.233540.18912001254100
4.509-4.930.224510.1841131118399.915
4.93-5.4940.273640.2079961060100
5.494-6.3110.315480.224914962100
6.311-7.6510.28440.232792836100
7.651-10.5060.245360.16862366099.848
10.506-31.060.424220.34441244298.19

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