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- PDB-1xmt: X-ray structure of gene product from arabidopsis thaliana at1g77540 -

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Basic information

Entry
Database: PDB / ID: 1xmt
TitleX-ray structure of gene product from arabidopsis thaliana at1g77540
Componentsputative acetyltransferase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PROTEIN STRUCTURE INITIATIVE / CESG / AT1G77540 / PUTATIVE ACETYLTRANSFERASE / PSI / Center for Eukaryotic Structural Genomics
Function / homology
Function and homology information


histone acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / peroxisome
Similarity search - Function
Yjdj-type Gcn5-related N-acetyltransferase / Gcn5-related N-acetyltransferase / GCN5-related N-acetyl-transferase / Yjdj-type Gcn5-related N-acetyltransferase (GNAT) domain profile. / Gcn5-related N-acetyltransferase (GNAT) / Acyl-CoA N-acyltransferase / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / Acetyltransferase At1g77540
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD (BROMIDE PHASING) / MAD / Resolution: 1.15 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: Biochemistry / Year: 2006
Title: Structure of Arabidopsis thaliana At1g77540 Protein, a Minimal Acetyltransferase from the COG2388 Family.
Authors: Tyler, R.C. / Bitto, E. / Berndsen, C.E. / Bingman, C.A. / Singh, S. / Lee, M.S. / Wesenberg, G.E. / Denu, J.M. / Phillips Jr., G.N. / Markley, J.L.
History
DepositionOct 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 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: putative acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,58712
Polymers11,7081
Non-polymers87911
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)27.349, 60.601, 29.424
Angle α, β, γ (deg.)90.00, 91.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein putative acetyltransferase


Mass: 11708.315 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At1g77540 / Plasmid details: derived from pQE / Plasmid: pVP13-GW / Production host: Escherichia coli (E. coli) / Strain (production host): BL834(DE3) pLacI+RARE / References: UniProt: Q9CAQ2
#2: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PROTEIN 10 MG/ML, 29% MEPEG 5K, 0.100 M SODIUM CITRATE, 0.100 M PIPES, CRYOPROTRECTED CRYSTAL SOAKED IN 1 M SODIUM BROMIDE FOR CIRCA 40 SECONDS, pH 6.5, Vapor diffusion, hanging drop, temperature 277 KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 0.926676, 0.926676, 0.919801, 0.919528, 0.91302
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Aug 8, 2004 / Details: RH MIRROR
RadiationMonochromator: DIAMOND 111 MIRROR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9266761
20.9198011
30.9195281
40.913021
ReflectionResolution: 1.15→20.29 Å / Num. obs: 32713 / % possible obs: 95.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.039 / Χ2: 0.944 / Net I/σ(I): 16.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allΧ2% possible all
1.15-1.181.90.3452.221606170.7
1.18-1.210.32419390.9585.7
1.21-1.240.32521330.90193.1
1.24-1.280.26321770.89697.4
1.28-1.320.23122290.91698.4
1.32-1.360.19622450.93398.6
1.36-1.420.1622180.91398.8
1.42-1.480.11622500.91199.1
1.48-1.560.08722540.91499.3
1.56-1.660.06822630.92499.6
1.66-1.790.05522640.96399.8
1.79-1.970.03822880.96899.9
1.97-2.250.02922641.008100
2.25-2.840.02522891100
2.84-500.0322940.97798.5

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
4
Phasing MADD res high: 2.49 Å / D res low: 25.11 Å / FOM : 0.77 / FOM acentric: 0.769 / FOM centric: 0.833 / Reflection: 6628
Phasing MAD set

Highest resolution: 2.49 Å / Lowest resolution: 25.11 Å

IDR cullisR cullis acentricR cullis centricR krautR kraut acentricR kraut centricFOM FOM acentricFOM centricLocLoc acentricLoc centricPower (kW)Power acentricPower centric
f_hpeak0.7140.7180.6150.0160.0160.0250.3160.3110.5213.13.13.2821.3451.3441.384
f_hpeak_FRIED0.6660.6670.640.0160.0160.0240.3570.3540.4853.2133.2133.4031.6611.661.711
f_peak0.6740.6840.4920.0130.0130.0260.3880.3790.7112.6962.6942.8991.5261.5251.554
f_peak_FRIED0.6260.6320.4920.0130.0120.0260.4140.4060.7052.6872.6862.8921.7791.7781.82
f_hrem0.8090.810.80.0130.0120.0160.2320.2340.1712.2762.2772.3951.0451.0451.068
f_hrem_FRIED0.6840.6820.7530.0120.0120.0170.3090.3160.0892.3462.3462.4941.5211.521.544
f_lrem_FRIED0.8360.822100.0090.00900.140.14501.6031.6031.6960.6630.6620.68
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)Atom typeF double prime refinedF prime refined
1110.926676BR2.37-3.25
1120.919801BR1.09-4.16
1130.919528BR1.64-2.14
1140.91302BR0.27-2
Phasing MAD set shell
IDResolution (Å)R cullisR cullis acentricR cullis centricR krautR kraut acentricR kraut centricFOM FOM acentricFOM centricLocLoc acentricLoc centricPower (kW)Power acentricPower centric
f_hpeak4.97-25.110.6460.6560.5220.0190.0180.0290.3510.3390.5944.0194.0444.0341.511.5021.633
f_hpeak3.95-4.970.7120.7180.5980.0140.0140.020.2790.2710.5063.9643.9693.9671.2471.2441.327
f_hpeak3.45-3.950.7140.7170.6240.0140.0140.0220.3220.3180.4733.4683.4733.4711.31.3061.091
f_hpeak3.14-3.450.7440.7450.7080.0140.0140.0280.3260.3170.6412.912.9132.9121.4321.431.491
f_hpeak2.91-3.140.7760.7730.9030.0160.0150.0290.3160.3120.4632.8332.8362.8351.2861.2940.991
f_hpeak2.74-2.910.7490.7520.6670.0180.0170.040.3250.3230.4292.5842.5872.5861.3771.381.207
f_hpeak2.6-2.740.7350.7320.9070.020.020.0220.3170.3140.4722.5572.5572.5571.2811.2821.237
f_hpeak2.49-2.60.7580.7541.0480.020.020.0150.2920.2890.4812.4462.452.4481.1781.1771.191
f_hpeak_FRIED4.97-25.110.5870.590.5420.020.0190.0280.3910.3840.5554.1544.184.1691.8741.8652.017
f_hpeak_FRIED3.95-4.970.6810.6830.640.0140.0140.020.3280.3230.4834.234.2354.2331.4991.4951.605
f_hpeak_FRIED3.45-3.950.6840.6850.6480.0140.0140.0220.3540.3520.4343.5883.5933.5911.6051.6121.345
f_hpeak_FRIED3.14-3.450.6980.6970.720.0140.0140.0280.3570.3510.5832.9742.9782.9761.7941.7911.891
f_hpeak_FRIED2.91-3.140.7170.7130.9240.0160.0150.0280.3530.3510.4282.8932.8962.8951.6151.6241.262
f_hpeak_FRIED2.74-2.910.6830.6830.6860.0180.0180.040.370.370.3972.6632.6672.6651.7081.7121.501
f_hpeak_FRIED2.6-2.740.6750.6710.9330.020.020.0210.3650.3630.4442.6162.6162.6161.6061.6081.535
f_hpeak_FRIED2.49-2.60.7240.721.1020.020.020.0140.3380.3360.4482.5752.5782.5771.4391.4391.48
f_peak4.97-25.110.6510.6730.4430.0170.0160.0340.390.3720.753.7883.8123.8021.5521.5421.714
f_peak3.95-4.970.7170.7230.5940.0110.0110.0190.340.330.6283.6213.6263.6241.321.3161.421
f_peak3.45-3.950.6910.7080.4230.0120.0110.0290.3650.3560.6743.1793.1833.1811.4041.4071.278
f_peak3.14-3.450.6490.6540.5380.0120.0110.0260.4140.4030.8182.482.4832.4821.6791.6751.806
f_peak2.91-3.140.7030.7060.6210.0130.0130.0250.3780.3670.7672.5192.5222.5211.4721.4811.144
f_peak2.74-2.910.670.6710.6120.0130.0130.0290.3990.3940.6642.1362.1392.1381.7281.7311.57
f_peak2.6-2.740.6090.6130.4950.0130.0130.020.4180.4140.5981.9091.9091.9091.8451.8481.744
f_peak2.49-2.60.6570.6610.5230.0140.0140.0180.4030.3960.7761.9071.911.9091.6331.6341.611
f_peak_FRIED4.97-25.110.590.6030.440.0170.0160.0330.4210.4060.7453.7613.7853.7751.8461.8352.039
f_peak_FRIED3.95-4.970.6790.6820.6110.0110.0110.0190.370.3620.6043.733.7343.7321.5081.5041.628
f_peak_FRIED3.45-3.950.6390.6530.4140.0120.0110.0280.3970.3890.6823.1093.1123.1111.6741.6781.505
f_peak_FRIED3.14-3.450.5940.5960.530.0110.0110.0260.4390.4290.7982.452.4532.4521.9721.9672.122
f_peak_FRIED2.91-3.140.6660.6680.6180.0130.0120.0240.4010.3910.7632.512.5132.5111.7061.7161.333
f_peak_FRIED2.74-2.910.6130.6130.5940.0120.0120.0290.4240.4190.6552.0762.0782.0772.0382.0421.845
f_peak_FRIED2.6-2.740.5620.5650.4880.0130.0120.0190.4440.440.611.8821.8821.8822.1342.1372.011
f_peak_FRIED2.49-2.60.6430.6460.5420.0140.0140.0180.4170.4120.7651.9751.9771.9761.7961.7971.782
f_hrem4.97-25.110.7310.7290.7560.0140.0140.0180.2690.2750.1872.7932.812.8031.2111.2051.299
f_hrem3.95-4.970.8140.8230.6510.0110.0110.0160.1910.1920.1762.9442.9482.9460.9480.9470.982
f_hrem3.45-3.950.840.8430.7490.0110.0110.0180.2230.2250.1652.7252.7282.7270.9420.9460.801
f_hrem3.14-3.450.8720.8661.1940.0120.0120.0140.2330.2350.1592.2482.252.2491.0671.0651.108
f_hrem2.91-3.140.8070.81.3110.0120.0120.0140.2430.2460.1641.9781.9811.981.0681.0750.824
f_hrem2.74-2.910.8040.81.0320.0140.0140.0240.2510.2530.1481.8691.8711.871.1081.110.989
f_hrem2.6-2.740.8430.8410.9180.0140.0140.0170.2280.2280.2161.8771.8771.8771.0291.030.993
f_hrem2.49-2.60.8360.8311.4360.0150.0150.010.2180.220.1121.7541.7561.7550.970.9681.04
f_hrem_FRIED4.97-25.110.6080.6040.6960.0140.0140.0180.3470.3630.0923.0073.0263.0181.7051.6981.832
f_hrem_FRIED3.95-4.970.6890.6880.7170.0110.0110.0150.2590.2660.0813.2273.2313.2291.3021.2991.371
f_hrem_FRIED3.45-3.950.7310.7360.5960.010.010.020.2840.290.0842.7912.7942.7931.3821.3881.156
f_hrem_FRIED3.14-3.450.7410.7341.1560.010.010.0140.3080.3140.0932.1672.172.1681.6651.6631.749
f_hrem_FRIED2.91-3.140.70.6921.3310.0120.0110.0150.3150.3220.0892.0282.032.0291.571.5791.222
f_hrem_FRIED2.74-2.910.6710.6671.050.0130.0130.0230.3360.3410.0751.8861.8881.8871.651.6541.447
f_hrem_FRIED2.6-2.740.6870.6830.8710.0130.0130.0170.3210.3260.1271.7991.7991.7991.6211.6231.539
f_hrem_FRIED2.49-2.60.7420.7371.5280.0150.0150.0090.3010.3060.0531.8571.861.8591.3961.3951.448
f_lrem_FRIED4.97-25.110.7060.686100.0090.0100.1670.17801.8771.8891.8840.8010.7970.854
f_lrem_FRIED3.95-4.970.7610.747100.0080.00900.1070.11102.2432.2462.2450.5480.5460.605
f_lrem_FRIED3.45-3.950.9280.914100.0070.00700.1040.10702.0112.0132.0120.5610.5640.468
f_lrem_FRIED3.14-3.450.9750.961100.0080.00800.1430.14701.5691.5711.570.6770.6750.733
f_lrem_FRIED2.91-3.140.8990.886100.0090.00900.1490.15401.3941.3951.3950.6920.6950.576
f_lrem_FRIED2.74-2.910.9270.918100.0090.00900.1440.14701.3371.3391.3380.7040.7060.598
f_lrem_FRIED2.6-2.740.9110.9100.010.0100.1630.16701.281.281.280.7090.7110.637
f_lrem_FRIED2.49-2.60.8720.864100.0090.0100.1480.15101.0891.0911.090.7610.760.795
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
15.6187550.68260.374151BR9.206351
21.75255-0.16372210.1411BR21.6171
34.8988753.74742.03917BR30.90251
49.5878318.7521.6646BR25.46851
512.465922.783627.621BR44.68821
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflection
4.97-25.110.78710.78920.8373830
3.95-4.970.72270.72170.7725832
3.45-3.950.740.73770.8504850
3.14-3.450.78180.77920.9014846
2.91-3.140.76540.76290.8854846
2.74-2.910.79360.79420.8096828
2.6-2.740.79290.79340.7751863
2.49-2.60.77630.77660.8189733
Phasing dmDelta phi final: 19.42 / Delta phi initial: 33.35 / FOM : 0.8817 / Mask type: RMS / Method: FLIP

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
CNSrefinement
REFMACrefmac_5.1.24refinement
PHENIXphasing
ARP/wARPmodel building
RefinementMethod to determine structure: MAD (BROMIDE PHASING) / Resolution: 1.15→30.303 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / WRfactor Rfree: 0.17 / WRfactor Rwork: 0.145 / SU B: 0.498 / SU ML: 0.023 / SU R Cruickshank DPI: 0.036 / Cross valid method: THROUGHOUT / ESU R Free: 0.035
RfactorNum. reflection% reflectionSelection details
Rfree0.1703 1658 5.072 %RANDOM
Rwork0.1476 ---
all0.149 ---
obs0.149 31030 95.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 17.748 Å2
Baniso -1Baniso -2Baniso -3
1--0.306 Å20 Å20.031 Å2
2--0.039 Å20 Å2
3---0.269 Å2
Refinement stepCycle: LAST / Resolution: 1.15→30.303 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms805 0 11 125 941
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021830
X-RAY DIFFRACTIONr_angle_refined_deg2.0221.9291124
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.835594
X-RAY DIFFRACTIONr_chiral_restr0.1520.2124
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.02612
X-RAY DIFFRACTIONr_nbd_refined0.2540.2471
X-RAY DIFFRACTIONr_nbtor_refined0.3260.2591
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2620.287
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2560.219
X-RAY DIFFRACTIONr_mcbond_it2.752485
X-RAY DIFFRACTIONr_mcangle_it3.964804
X-RAY DIFFRACTIONr_scbond_it4.6686345
X-RAY DIFFRACTIONr_scangle_it6.7888320
X-RAY DIFFRACTIONSphericity. Free atoms6.7922136
X-RAY DIFFRACTIONSphericity. Bonded atoms6.3212805
X-RAY DIFFRACTIONRigid bond restraints2.3822830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-IDNum. reflection all
1.15-1.17940.318880.291713X-RAY DIFFRACTION2504
1.179-1.21170.2261170.2361998X-RAY DIFFRACTION2426
1.212-1.24680.2551090.2112147X-RAY DIFFRACTION2400
1.247-1.28510.1651050.1722130X-RAY DIFFRACTION2295
1.285-1.32710.1851170.1512080X-RAY DIFFRACTION2224
1.327-1.37360.1511120.1452051X-RAY DIFFRACTION2193
1.374-1.42540.133950.1361961X-RAY DIFFRACTION2078
1.425-1.48340.157950.1271905X-RAY DIFFRACTION2020
1.483-1.54920.13940.1191825X-RAY DIFFRACTION1932
1.549-1.62460.158900.1181751X-RAY DIFFRACTION1849
1.625-1.71220.161860.1171672X-RAY DIFFRACTION1763
1.712-1.81570.153790.121581X-RAY DIFFRACTION1663
1.816-1.94060.145750.1291499X-RAY DIFFRACTION1574
1.941-2.09540.163850.1351384X-RAY DIFFRACTION1469
2.095-2.29430.167680.1391270X-RAY DIFFRACTION1338
2.294-2.56320.181750.1461130X-RAY DIFFRACTION1205
2.563-2.95620.185500.1561034X-RAY DIFFRACTION1084
2.956-3.6120.179530.15860X-RAY DIFFRACTION915
3.612-5.07230.143440.145661X-RAY DIFFRACTION721
5.072-30.3030.225210.198378X-RAY DIFFRACTION414

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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