[English] 日本語
Yorodumi
- PDB-2p35: Crystal structure of trans-aconitate methyltransferase from Agrob... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2p35
TitleCrystal structure of trans-aconitate methyltransferase from Agrobacterium tumefaciens
ComponentsTrans-aconitate 2-methyltransferase
KeywordsTRANSFERASE / trans-aconitate methyltransferase / SAM dependent methyltransferase / Agrobacterium tumefaciens / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


trans-aconitate 2-methyltransferase / trans-aconitate 2-methyltransferase activity / methylation / cytoplasm
Similarity search - Function
S-adenosyl-L-methionine-dependent methyltransferases / Trans-aconitate 2-methyltransferase, C-terminal / Trans-aconitate 2-methyltransferase / Vaccinia Virus protein VP39 / DNA polymerase; domain 1 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Trans-aconitate 2-methyltransferase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens str. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsChang, C. / Xu, X. / Zheng, H. / Savchenko, A. / Edwards, A.M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of trans-aconitate methyltransferase from Agrobacterium tumefaciens
Authors: Chang, C. / Xu, X. / Zheng, H. / Savchenko, A. / Joachimiak, A.
History
DepositionMar 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 14, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Trans-aconitate 2-methyltransferase
B: Trans-aconitate 2-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0124
Polymers58,2442
Non-polymers7692
Water7,260403
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.097, 103.097, 107.457
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

-
Components

#1: Protein Trans-aconitate 2-methyltransferase /


Mass: 29121.797 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens str. (bacteria)
Species: Agrobacterium tumefaciens / Strain: C58 / Gene: tam, Atu0870, AGR_C_1589 / Plasmid: pET derivative / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) derivative
References: UniProt: Q8UH15, trans-aconitate 2-methyltransferase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 403 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.52 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Na(OAC) pH 4.5, 25% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2007
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 47410 / Num. obs: 47098 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 10.5 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 30.65
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 1.6 / % possible all: 93.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→41.24 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.945 / SU B: 6.016 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21435 2376 5.1 %RANDOM
Rwork0.18564 ---
obs0.18713 44665 99.26 %-
all-44665 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.538 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20.25 Å20 Å2
2--0.5 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 1.95→41.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 52 403 4253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224149
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.241.9765700
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5245529
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.84724.354209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57715654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1961530
X-RAY DIFFRACTIONr_chiral_restr0.0930.2611
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023299
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1930.21936
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22753
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2360
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2460.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8951.52598
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04524075
X-RAY DIFFRACTIONr_scbond_it2.01331808
X-RAY DIFFRACTIONr_scangle_it2.794.51601
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 170 -
Rwork0.263 3015 -
obs--91.44 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
127.2644-14.7536-5.599110.64893.9286.54380.02720.43740.5478-0.2958-0.2854-0.4717-0.791-0.29940.2582-0.05460.0303-0.0921-0.0532-0.0063-0.1046-30.55757.68715.301
25.20653.05490.6633.90950.99822.49690.040.28440.41820.0513-0.06110.2059-0.2023-0.04820.0211-0.0780.01360.0091-0.02150.0489-0.0431-13.85453.48819.545
33.5112-0.7447-1.66545.259-1.11943.9470.04160.64180.1283-0.4845-0.2314-0.2827-0.0083-0.26450.1898-0.08730.02990.06730.02870.0963-0.1043-5.40953.3616.973
41.71-0.0614-0.13740.8409-0.76281.8847-0.00270.12360.07560.0359-0.1561-0.27560.05070.13070.1588-0.10240.0041-0.0070.01240.05070.0253-0.6746.86422.645
51.40840.75871.47144.3741.37324.0630.11180.2668-0.1409-0.15590.0558-0.59770.39440.4397-0.16760.020.04180.0091-0.0023-0.0193-0.0265-18.37624.14611.545
64.71643.09521.88092.28841.4841.109-0.05630.07370.0473-0.0937-0.09010.26870.0092-0.00960.14650.021-0.0212-0.03080.0724-0.04710.0287-26.42337.21919.585
76.8274-4.71614.81144.9646-2.23135.6162-0.0080.03380.5674-0.1159-0.0859-0.2806-0.3160.01430.0939-0.0754-0.0405-0.0095-0.0528-0.0496-0.0521-22.68956.24228.547
82.741-0.1342-0.88224.65520.93995.2358-0.1111-0.31560.27410.382-0.15-0.0424-0.5414-0.17940.2611-0.03230.0223-0.0898-0.0618-0.1326-0.0897-31.07764.21538.103
91.4802-0.2088-0.10032.7461.36981.596-0.0273-0.15990.02120.0506-0.28610.42650.0233-0.36960.3134-0.1016-0.0137-0.01660.0731-0.1039-0.0332-35.88249.31330.085
100.79490.3677-1.05861.462-0.03745.9093-0.1547-0.23-0.02240.01010.02030.21370.1023-0.27630.1345-0.04060.00620.03450.03030.0034-0.0788-18.33139.752.983
117.613-0.53214.37250.093-0.14292.9861-0.2516-0.15270.0793-0.03320.0448-0.0833-0.04740.06220.20670.0028-0.0211-0.03390.0786-0.004-0.0393-9.81844.1838.627
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 148 - 17
2X-RAY DIFFRACTION2AA15 - 2918 - 32
3X-RAY DIFFRACTION3AA30 - 8433 - 87
4X-RAY DIFFRACTION4AA85 - 12988 - 132
5X-RAY DIFFRACTION4AA164 - 185167 - 188
6X-RAY DIFFRACTION4AA250 - 256253 - 259
7X-RAY DIFFRACTION5AA130 - 163133 - 166
8X-RAY DIFFRACTION5AA194 - 234197 - 237
9X-RAY DIFFRACTION6AA186 - 193189 - 196
10X-RAY DIFFRACTION6AA235 - 249238 - 252
11X-RAY DIFFRACTION7BB15 - 2918 - 32
12X-RAY DIFFRACTION8BB30 - 8433 - 87
13X-RAY DIFFRACTION9BB85 - 12988 - 132
14X-RAY DIFFRACTION9BB164 - 185167 - 188
15X-RAY DIFFRACTION9BB250 - 256253 - 259
16X-RAY DIFFRACTION10BB130 - 163133 - 166
17X-RAY DIFFRACTION10BB194 - 234197 - 237
18X-RAY DIFFRACTION11BB186 - 193189 - 196
19X-RAY DIFFRACTION11BB235 - 249238 - 252

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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

-
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

Read more