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- PDB-2exr: X-Ray Structure of Cytokinin Oxidase/Dehydrogenase (CKX) From Ara... -

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Basic information

Entry
Database: PDB / ID: 2exr
TitleX-Ray Structure of Cytokinin Oxidase/Dehydrogenase (CKX) From Arabidopsis Thaliana AT5G21482
ComponentsCytokinin dehydrogenase 7
KeywordsOXIDOREDUCTASE / At5g21482.1 / CYTOKININ OXIDASE/DEHYDROGENASE / CKX / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / PSI / CENTER FOR EUKARYOTIC STRUCTURAL GENOMICS / CESG
Function / homology
Function and homology information


cytokinin catabolic process / cytokinin dehydrogenase / cytokinin dehydrogenase activity / FAD binding / cytosol
Similarity search - Function
Cytokinin dehydrogenase 1, FAD/cytokinin binding domain / Cytokinin dehydrogenase 1, FAD and cytokinin binding / : / FAD-linked oxidases, C-terminal domain / Cytokinin dehydrogenase, C-terminal domain superfamily / Vanillyl-alcohol Oxidase; Chain A, domain 3 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 ...Cytokinin dehydrogenase 1, FAD/cytokinin binding domain / Cytokinin dehydrogenase 1, FAD and cytokinin binding / : / FAD-linked oxidases, C-terminal domain / Cytokinin dehydrogenase, C-terminal domain superfamily / Vanillyl-alcohol Oxidase; Chain A, domain 3 / FAD-linked oxidase-like, C-terminal / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 2 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Cytokinin dehydrogenase 7
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.702 Å
AuthorsWesenberg, G.E. / Phillips Jr., G.N. / Han, B.W. / Bitto, E. / Bingman, C.A. / Bae, E. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: Proteins / Year: 2008
Title: Crystal structure of Arabidopsis thaliana cytokinin dehydrogenase.
Authors: Bae, E. / Bingman, C.A. / Bitto, E. / Aceti, D.J. / Phillips, G.N.
History
DepositionNov 8, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2005Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2012Group: Database references
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Nov 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_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: Cytokinin dehydrogenase 7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1512
Polymers58,3651
Non-polymers7861
Water11,403633
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.858, 114.502, 190.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Cytokinin dehydrogenase 7 / Cytokinin oxidase 7 / CKO7 / AtCKX7 / AtCKX5


Mass: 58365.340 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: CKX7, CKX5 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q9FUJ1, cytokinin dehydrogenase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / 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: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Protein solution (10 mg/ml protein, 0.10 M Bis Tris, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, pH 7.0) mixed in a 1:1 ratio with the well solution (24% MEPEG 5K, 0.05 M ...Details: Protein solution (10 mg/ml protein, 0.10 M Bis Tris, 0.050 M sodium chloride, 0.0031 M sodium azide, 0.0003 M TCEP, pH 7.0) mixed in a 1:1 ratio with the well solution (24% MEPEG 5K, 0.05 M magnesium sulfate, 0.1 M HEPPS pH 8.5),temperature 277K, vapor diffusion, hanging drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97911, 0.96403
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2005
Details: HORIZONTAL SAGITALLY FOCUSING 2ND BENT MONOCHROMATOR CRYSTAL, VERTICAL BENT FOCUSING MIRROR
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1CRYOGENICALLY COOLED SI (220) DOUBLE BOUNCEMADMx-ray1
2Mx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.979111
20.964031
Reflection

D res high: 1.7 Å / D res low: 80 Å

Redundancy (%)IDNumberRmerge(I) obsΧ2% possible obs
6.81529610.0911.27795.1
6.72520930.0871.06793.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
3.668099.610.0831.2917
2.913.6699.910.0861.3757.3
2.542.9110010.091.2927.4
2.312.5410010.11.3287.4
2.142.3110010.1071.4377.4
2.022.1410010.1171.3277.2
1.912.029910.1381.2296.8
1.831.9193.710.1611.116.1
1.761.8384.410.1961.0635.7
1.71.7673.410.2321.084.8
3.668099.520.0741.0887
2.913.6699.920.0771.0257.4
2.542.9199.920.0881.0187.4
2.312.5410020.0951.1887.5
2.142.3110020.1111.057.4
2.022.1499.920.1381.1327.1
1.912.0297.220.2341.16.5
1.831.9187.820.1920.9965.9
1.761.8379.520.2390.9455.4
1.71.7669.920.2841.0394.8
ReflectionResolution: 1.7→42.57 Å / Num. obs: 52961 / % possible obs: 95.1 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.091 / Χ2: 1.277 / Net I/σ(I): 10.709
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 4.373 / Num. unique all: 4054 / Χ2: 1.08 / % possible all: 73.4

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Phasing

PhasingMethod: MAD
Phasing MAD set

Highest resolution: 1.7 Å / Lowest resolution: 42.56 Å

IDR cullis acentricR cullis centricPower acentricPower centricReflection acentricReflection centric
ISO_10000481034216
ISO_20.7820.751.0240.847468694116
ANO_10.76201.1830467720
ANO_20.87600.6850457580
Phasing MAD set shell
IDResolution (Å)R cullis acentricR cullis centricPower acentricPower centricReflection acentricReflection centric
ISO_17.5-42.560000497219
ISO_15.34-7.50000983232
ISO_14.37-5.3400001277232
ISO_13.79-4.3700001544228
ISO_13.4-3.7900001748225
ISO_13.1-3.400001960237
ISO_12.87-3.100002147216
ISO_12.69-2.8700002311238
ISO_12.53-2.6900002479213
ISO_12.4-2.5300002626209
ISO_12.29-2.400002732194
ISO_12.2-2.2900002920227
ISO_12.11-2.200003030210
ISO_12.03-2.1100003131221
ISO_11.96-2.0300003258211
ISO_11.9-1.9600003282219
ISO_11.85-1.900003311197
ISO_11.79-1.8500003133177
ISO_11.75-1.7900003007167
ISO_11.7-1.7500002727144
ANO_17.5-42.560.6801.26504970
ANO_15.34-7.50.63301.51209830
ANO_14.37-5.340.76601.228012770
ANO_13.79-4.370.801.101015400
ANO_13.4-3.790.76201.233017450
ANO_13.1-3.40.72801.296019560
ANO_12.87-3.10.68901.449021450
ANO_12.69-2.870.67101.554023080
ANO_12.53-2.690.68301.551024770
ANO_12.4-2.530.6901.457026250
ANO_12.29-2.40.73401.355027300
ANO_12.2-2.290.74701.213029190
ANO_12.11-2.20.78101.116030300
ANO_12.03-2.110.81501.009031290
ANO_11.96-2.030.86100.886032450
ANO_11.9-1.960.88700.782031970
ANO_11.85-1.90.91500.707031160
ANO_11.79-1.850.92600.666028840
ANO_11.75-1.790.94300.604026810
ANO_11.7-1.750.95800.541022880
ISO_27.5-42.560.6710.611.521.189497218
ISO_25.34-7.50.6560.6741.7821.151983230
ISO_24.37-5.340.7220.7331.2580.851276229
ISO_23.79-4.370.7420.7881.0860.7811541228
ISO_23.4-3.790.7430.7121.1320.8071747223
ISO_23.1-3.40.7160.7591.1690.8511960236
ISO_22.87-3.10.7220.7281.310.8992147215
ISO_22.69-2.870.7170.7661.3460.8982311236
ISO_22.53-2.690.740.7921.3310.9582479213
ISO_22.4-2.530.7160.7291.2930.882626209
ISO_22.29-2.40.7660.7721.1770.8222732193
ISO_22.2-2.290.8010.7811.030.7072920227
ISO_22.11-2.20.8210.8410.8970.6163030210
ISO_22.03-2.110.8390.8740.7580.5263129220
ISO_21.96-2.030.8750.9320.6330.4343220203
ISO_21.9-1.960.8760.9120.5440.3983169202
ISO_21.85-1.90.9120.9610.5010.4223057181
ISO_21.79-1.850.9190.9550.4830.4042854161
ISO_21.75-1.790.8990.9910.4210.4232736150
ISO_21.7-1.750.8910.8940.4050.3632455132
ANO_27.5-42.560.78200.84404970
ANO_25.34-7.50.73601.01309830
ANO_24.37-5.340.83500.836012760
ANO_23.79-4.370.87400.769015370
ANO_23.4-3.790.85500.795017470
ANO_23.1-3.40.84200.831019590
ANO_22.87-3.10.80500.913021460
ANO_22.69-2.870.80400.893023110
ANO_22.53-2.690.8200.889024790
ANO_22.4-2.530.83500.809026250
ANO_22.29-2.40.86400.722027320
ANO_22.2-2.290.89600.648029200
ANO_22.11-2.20.91600.56030300
ANO_22.03-2.110.93300.467031180
ANO_21.96-2.030.95500.396031590
ANO_21.9-1.960.96500.373030390
ANO_21.85-1.90.96500.357028670
ANO_21.79-1.850.97300.333026370
ANO_21.75-1.790.9800.299024800
ANO_21.7-1.750.98400.282022160
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
110.87536.316-151.566SE20.080.99
27.42637.4160.352SE19.211.17
310.63428.952-154.378SE23.360.92
417.21849.268-63.389SE43.550.84
55.61731.741-67.734SE23.230.92
67.49346.96-150.74SE26.90.94
78.0455.802-28.729SE25.680.9
82.5868.7650.512SE41.210.63
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 52916
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
8.5-10059.10.864517
6.25-8.5560.931725
5.17-6.2553.60.925898
4.51-5.1757.30.9331047
4.05-4.5158.10.9311164
3.71-4.0559.40.9181287
3.44-3.7156.30.9231367
3.22-3.4457.80.9151475
3.04-3.2256.50.9131552
2.89-3.0456.50.8971643
2.76-2.8959.80.9021744
2.64-2.7657.10.8931795
2.54-2.6455.40.8891855
2.45-2.5455.70.891950
2.37-2.4559.50.8881993
2.29-2.3759.50.882039
2.22-2.2959.40.8812185
2.16-2.2259.30.882193
2.11-2.1661.50.8762249
2.05-2.1161.40.8682301
2-2.0564.80.8562365
1.96-266.40.852439
1.92-1.9669.10.8512388
1.88-1.9270.10.832442
1.84-1.88720.8312368
1.8-1.8470.10.7952292
1.77-1.872.90.7952185
1.74-1.7775.70.7912158
1.7-1.7477.40.7372300

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMACrefmac_5.2.0005refinement
PDB_EXTRACT1.701data extraction
PHENIXphasing
SHELXDphasing
SOLOMONphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.702→42.57 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.952 / WRfactor Rfree: 0.241 / WRfactor Rwork: 0.188 / SU B: 2.208 / SU ML: 0.075 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.115
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, SELENIUM C COEFFICIENT FOR STRUCTURE FACTOR CALCULATION SET TO -9.00, MOLPROBITY USED TO ASSIST IN FINAL MODEL BUILDING.
RfactorNum. reflection% reflectionSelection details
Rfree0.2139 2669 5.044 %RANDOM
Rwork0.1712 ---
all0.173 ---
obs0.17331 52917 95.086 %-
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: 26.484 Å2
Baniso -1Baniso -2Baniso -3
1--0.098 Å20 Å20 Å2
2--1.633 Å20 Å2
3----1.535 Å2
Refinement stepCycle: LAST / Resolution: 1.702→42.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3853 0 53 633 4539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224223
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9675795
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6085553
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94923.397209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12115695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4781539
X-RAY DIFFRACTIONr_chiral_restr0.0970.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023309
X-RAY DIFFRACTIONr_nbd_refined0.1980.22092
X-RAY DIFFRACTIONr_nbtor_refined0.3070.22909
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2524
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.236
X-RAY DIFFRACTIONr_mcbond_it1.27722595
X-RAY DIFFRACTIONr_mcangle_it2.09644127
X-RAY DIFFRACTIONr_scbond_it3.33161886
X-RAY DIFFRACTIONr_scangle_it4.64381635
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
1.702-1.7460.2621300.22227620.224401971.958
1.746-1.7940.2571910.20830100.211397880.468
1.794-1.8460.2561800.20331560.206383586.988
1.846-1.9020.2331620.19433910.196378293.945
1.902-1.9650.2411860.18833420.191360497.891
1.965-2.0340.2391760.19133510.193353599.774
2.034-2.110.2311720.18132360.184340999.971
2.11-2.1970.2351840.18531120.1883296100
2.197-2.2940.2071570.18230190.1843176100
2.294-2.4060.231580.18128260.1842984100
2.406-2.5360.261330.18327370.1862870100
2.536-2.690.2221280.18525910.187272099.963
2.69-2.8760.2221340.17924430.1812577100
2.876-3.1060.2241070.17522750.177238599.874
3.106-3.4020.2071110.15621020.159221599.91
3.402-3.8030.194970.14519130.147201399.851
3.803-4.390.174900.13317020.1351792100
4.39-5.3730.16760.14114460.142152399.934
5.373-7.5870.188590.18311710.1831230100
7.587-95.3460.215380.1816630.18370998.872

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