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- PDB-1y0z: X-ray structure of gene product from Arabidopsis thaliana At3g21360 -

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Basic information

Entry
Database: PDB / ID: 1y0z
TitleX-ray structure of gene product from Arabidopsis thaliana At3g21360
Componentsprotein product of AT3G21360
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PROTEIN STRUCTURE INITIATIVE / PSI / CESG / AT3G21360 / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


Oxidoreductases / oxidoreductase activity / nucleus / metal ion binding / cytosol
Similarity search - Function
Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Clavaminate synthase-like protein At3g21360
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsWesenberg, G.E. / Phillips Jr., G.N. / Bitto, E. / Bingman, C.A. / Allard, S.T.M. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2005
Title: The structure at 2.4 A resolution of the protein from gene locus At3g21360, a putative Fe(II)/2-oxoglutarate-dependent enzyme from Arabidopsis thaliana.
Authors: Bitto, E. / Bingman, C.A. / Allard, S.T. / Wesenberg, G.E. / Aceti, D.J. / Wrobel, R.L. / Frederick, R.O. / Sreenath, H. / Vojtik, F.C. / Jeon, W.B. / Newman, C.S. / Primm, J. / Sussman, M.R. ...Authors: Bitto, E. / Bingman, C.A. / Allard, S.T. / Wesenberg, G.E. / Aceti, D.J. / Wrobel, R.L. / Frederick, R.O. / Sreenath, H. / Vojtik, F.C. / Jeon, W.B. / Newman, C.S. / Primm, J. / Sussman, M.R. / Fox, B.G. / Markley, J.L. / Phillips, G.N.
History
DepositionNov 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Version format compliance
Revision 1.4Nov 16, 2011Group: Atomic model
Revision 1.5Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.6Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE ...THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN AND THE TWO CHAINS IN THE ASYMMETRIC UNIT MAY NOT REPRESENT THE BIOLOGICAL UNIT.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: protein product of AT3G21360
B: protein product of AT3G21360
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,0178
Polymers74,5212
Non-polymers4966
Water14,052780
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)145.276, 61.094, 114.681
Angle α, β, γ (deg.)90.00, 121.68, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1301-

HOH

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Components

#1: Protein protein product of AT3G21360


Mass: 37260.449 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At3g21360 / Plasmid: pVP-17 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q9LIG0
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 780 / 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 (%)
12.957.64
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, hanging drop7.510 MG/ML PROTEIN, 16% GLYCEROL, 1.80 M AMMONIUM SULFATE, 0.100 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
2772vapor diffusion, hanging drop7.510 MG/ML PROTEIN, 15% GLYCEROL, 1.75 M AMMONIUM SULFATE, 0.100 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-BM10.97954
SYNCHROTRONAPS 14-ID-B20.97927
Detector
TypeIDDetectorDateDetails
APS-11CCDJul 31, 2004sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
MAR CCD 165 mm2CCDOct 25, 2004bent cylindrical Si-mirror (Rh coating)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Rosenbaum-Rock double-crystal monochromator, water cooledSINGLE WAVELENGTHMx-ray1
2Diamond (111) double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979541
20.979271
ReflectionResolution: 2.39→43.63 Å / Num. all: 34020 / Num. obs: 34020 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 22.8 Å2 / Limit h max: 51 / Limit h min: -60 / Limit k max: 25 / Limit k min: -60 / Limit l max: 47 / Limit l min: 0 / Observed criterion F max: 279052.43 / Observed criterion F min: 0.32 / Rmerge(I) obs: 0.079 / Net I/σ(I): 12.572
Reflection shell

Mean I/σ(I) obs: 4.451 / Diffraction-ID: 1,2 / Redundancy: 3.5 %

Resolution (Å)Rmerge(I) obsNum. measured allΧ2% possible all
2.4-2.460.28322500.86599.9
2.46-2.520.26722330.9100
2.52-2.590.24522310.929100
2.59-2.660.22522970.98100
2.66-2.750.21722301.143100
2.75-2.850.17522531.138100
2.85-2.960.13722561.085100
2.96-3.090.10822741.109100
3.09-3.260.09322721.11199.9
3.26-3.460.07322711.052100
3.46-3.730.05822631.002100
3.73-4.10.04922940.995100
4.1-4.70.04322770.9799.3
4.7-5.920.04422741.0299.6
5.92-500.0323451.04698.9

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 3.69 Å / D res low: 43.52 Å / FOM : 0.351 / FOM acentric: 0.367 / FOM centric: 0 / Reflection: 17720
Phasing MAD setR cullis: 0.692 / R cullis acentric: 0.676 / R cullis centric: 10 / R kraut: 0.023 / R kraut acentric: 0.023 / R kraut centric: 0.005 / Highest resolution: 3.69 Å / Lowest resolution: 43.52 Å / FOM : 0.353 / FOM acentric: 0.369 / FOM centric: 0 / Loc: 16.521 / Loc acentric: 16.526 / Loc centric: 16.555 / Power: 1.547 kW / Power acentric: 1.542 / Power centric: 1.653
Phasing MAD setWavelength: 0.97927 Å / Atom type: SE / F double prime refined: 2.28 / F prime refined: -11
Phasing MAD set shell

ID: f_peak_FRIED / R cullis centric: 10 / FOM centric: 0

Resolution (Å)R cullisR cullis acentricR krautR kraut acentricR kraut centricFOM FOM acentricLocLoc acentricLoc centricPower (kW)Power acentricPower centric
7.37-43.520.6430.6140.0270.0290.0070.3720.40817.80517.8317.8191.8621.871.781
5.85-7.370.5770.5610.0310.0320.0070.4080.43115.22215.22915.2262.0142.0062.159
5.12-5.850.5970.5830.0260.0260.0080.4010.4214.75414.75414.7541.8711.8612.071
4.65-5.120.6480.6350.0190.020.0030.3910.40715.63515.64215.6391.6081.6111.521
4.32-4.650.7290.7160.0190.0190.0030.3370.3516.00316.0116.0071.431.431.432
4.06-4.320.7610.7480.0180.0190.0020.320.33216.85416.85416.8541.2781.2771.3
3.86-4.060.7950.7830.0210.0210.0020.3130.32317.43617.43617.4361.1921.1971.036
3.69-3.860.8540.8410.0230.0230.0050.2730.28218.61618.62518.6211.0531.0531.068
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
147.0945-40.90040.004405897SE16.44991
275.2987-44.455138.1047SE24.51131
315.6163-34.079937.1413SE25.7711
437.3727-44.482890.4684SE33.17281
544.8684-54.616476.5589SE53.61441
668.868-41.021340.117SE49.19481
756.2694-51.162584.2961SE47.81991
825.5662-31.003343.7895SE75.81581
944.0097-54.51582.014SE84.97141
1021.0149-30.946147.6547SE00.317548
1113.9938-41.994739.8289SE00.241042
1230.5073-31.851722.6074SE00.185791
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflection
7.37-43.520.36990.405302222
5.85-7.370.40720.429902240
5.12-5.850.39970.418502211
4.65-5.120.3890.404602221
4.32-4.650.3360.348102255
4.06-4.320.31860.329902213
3.86-4.060.31230.321602252
3.69-3.860.27080.279502106
Phasing dmFOM : 0.63 / FOM acentric: 0.64 / FOM centric: 0.61 / Reflection: 33929 / Reflection acentric: 32025 / Reflection centric: 1904
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
6.8-43.5090.90.90.7915111287224
4.3-6.80.870.880.7645804225355
3.4-4.30.850.860.7656815336345
3-3.40.730.740.6157715480291
2.6-30.510.510.45101929745447
2.4-2.60.320.320.3161945952242

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RESOLVE2.05phasing
CNS1.1refinement
PDB_EXTRACT1data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.4→43.63 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 0.65 / Cross valid method: THROUGHOUT / Details: Molprobity used to assist in final model building
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1628 5 %RANDOM
Rwork0.193 ---
all-33755 --
obs-32733 97 %-
Solvent computationSolvent model: bulk solvent model / Bsol: 56.3737 Å2 / ksol: 0.349677 e/Å3
Displacement parametersBiso max: 150.4 Å2 / Biso mean: 35.6 Å2 / Biso min: 2.75 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å20 Å24.42 Å2
2---0.37 Å20 Å2
3----2.22 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.4→43.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5139 0 22 780 5941
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg23.7
X-RAY DIFFRACTIONx_torsion_impr_deg0.92
X-RAY DIFFRACTIONx_mcbond_it6.081.5
X-RAY DIFFRACTIONx_mcangle_it9.432
X-RAY DIFFRACTIONx_scbond_it9.62
X-RAY DIFFRACTIONx_scangle_it13.482.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.4-2.510.3372075.30.26536810.0234172388893.2
2.51-2.640.2872055.20.23637510.024206395694.1
2.64-2.810.2892045.10.23537880.024193399295.2
2.81-3.020.27820650.20438820.0194202408897.3
3.02-3.330.2672165.20.19839140.0184205413098.2
3.33-3.810.2171954.60.17740100.0164235420599.3
3.81-4.80.1711964.70.13939990.0124233419599.1
4.8-43.630.2311994.70.240800.0164341427998.6
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.param

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