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- PDB-1ybm: X-ray structure of selenomethionyl gene product from Arabidopsis ... -

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Basic information

Entry
Database: PDB / ID: 1ybm
TitleX-ray structure of selenomethionyl gene product from Arabidopsis thaliana at5g02240 in space group P21212
Componentsunknown protein At5g02240
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PROTEIN STRUCTURE INITIATIVE / CESG / PSI / Center for Eukaryotic Structural Genomics / NADP
Function / homology
Function and homology information


apoplast / response to abscisic acid / 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: 2.096 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 selenomethionyl gene product from Arabidopsis thaliana at5g02240 in space group P21212
Authors: Center for Eukaryotic Structural Genomics (CESG)
History
DepositionDec 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: unknown protein At5g02240
B: unknown protein At5g02240
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6724
Polymers54,1862
Non-polymers1,4872
Water6,648369
1
A: unknown protein At5g02240
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 At5g02240
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)74.634, 77.286, 92.864
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B

NCS domain segments:

Ens-ID: 1 / Refine code: 6

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAVALVALAA2 - 802 - 80
21ALAALAVALVALBB2 - 802 - 80
32GLYGLYPHEPHEAA102 - 253102 - 253
42GLYGLYPHEPHEBB102 - 253102 - 253

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Components

#1: Protein unknown protein At5g02240


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-17 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q94EG6
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


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


Mass: 18.015 Da / Num. of mol.: 369 / 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: 2.5 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10 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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-ID-B / Wavelength: 0.97935, 0.97904, 0.96389
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 8, 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 wavelength
IDWavelength (Å)Relative weight
10.979351
20.979041
30.963891
ReflectionResolution: 2.096→29.087 Å / Num. obs: 29937 / % possible obs: 93 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.047 / Χ2: 1.051 / Net I/σ(I): 22.745
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allΧ2% possible all
2.1-2.159.30.286.12518781.03188.3
2.15-2.20.25119520.9992.9
2.2-2.260.25620101.07595.3
2.26-2.330.21620340.9996.1
2.33-2.40.1620001.02995.7
2.4-2.490.13720321.06594.8
2.49-2.590.11620221.06395.4
2.59-2.710.0920171.11195.3
2.71-2.850.07420221.15394.8
2.85-3.030.06120101.16893.8
3.03-3.260.0520041.03793.3
3.26-3.590.03720071.01493
3.59-4.110.0319980.97692.1
4.11-5.180.02719841.0490.1
5.18-500.03319671.00884.8

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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
three wavelength110.97951.3-10.73
three wavelength120.97924.28-8.04
three wavelength130.96413.31-3.89
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
PDB_EXTRACT1data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.096→29.09 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.916 / WRfactor Rfree: 0.266 / WRfactor Rwork: 0.191 / SU B: 6.058 / SU ML: 0.161 / SU R Cruickshank DPI: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, MOLPROBITY USED TO ASSIST IN FINAL MODEL BUILDING
RfactorNum. reflection% reflectionSelection details
Rfree0.2615 1525 5.108 %RANDOM
Rwork0.1888 ---
all0.193 ---
obs-29855 92.634 %-
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: 38.303 Å2
Baniso -1Baniso -2Baniso -3
1--1.539 Å20 Å20 Å2
2--1.589 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 2.096→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3672 0 96 369 4137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0223834
X-RAY DIFFRACTIONr_angle_refined_deg1.6432.0075196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5925482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.88425.789152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08615664
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3821514
X-RAY DIFFRACTIONr_chiral_restr0.1060.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022804
X-RAY DIFFRACTIONr_nbd_refined0.2040.21861
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22578
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1980.2339
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3060.235
X-RAY DIFFRACTIONr_mcbond_it3.2242486
X-RAY DIFFRACTIONr_mcangle_it4.41263848
X-RAY DIFFRACTIONr_scbond_it6.38381531
X-RAY DIFFRACTIONr_scangle_it8.126121348
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1734 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
loose positional0.395
loose thermal6.1710
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 (%)
2.096-2.150.327990.2361869235183.709
2.15-2.2090.3481070.2262017229592.549
2.209-2.2730.3141240.2291987221095.52
2.273-2.3430.322850.2351988216595.751
2.343-2.420.3840.2171916209295.602
2.42-2.5050.325970.2191851203695.678
2.505-2.5990.284970.2211774196595.216
2.599-2.7050.271930.2021709189395.193
2.705-2.8260.304930.1981638182594.849
2.826-2.9630.289910.1971547174393.976
2.963-3.1240.332790.21469165593.535
3.124-3.3130.243770.1861405157694.036
3.313-3.5410.266770.1741305149092.752
3.541-3.8250.225700.1641219139392.534
3.825-4.1890.227640.1561117129391.338
4.189-4.6820.217610.146998117090.513
4.682-5.4040.203490.163878103489.652
5.404-6.6130.283400.20175589888.53
6.613-9.3290.222310.18258171785.356
9.329-92.8480.08170.21530742873.364

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