[English] 日本語
Yorodumi
- PDB-3cj8: Crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cj8
TitleCrystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase from Enterococcus faecalis V583
Components2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase
KeywordsTRANSFERASE / APC86892 / 2 / 3 / 4 / 5-tetrahydropyridine-2-carboxylate N-succinyltransferase / Enterococcus faecalis V583 / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


tetrahydrodipicolinate N-acetyltransferase / tetrahydrodipicolinate N-acetyltransferase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate
Similarity search - Function
Black beetle virus capsid protein - #10 / Black beetle virus capsid protein / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase, N-terminal / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase, DapH / Tetrahydrodipicolinate succinyltransferase N-terminal / Malonyl-CoA ACP transacylase, ACP-binding / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins ...Black beetle virus capsid protein - #10 / Black beetle virus capsid protein / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase, N-terminal / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase, DapH / Tetrahydrodipicolinate succinyltransferase N-terminal / Malonyl-CoA ACP transacylase, ACP-binding / Hexapeptide repeat of succinyl-transferase / Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Few Secondary Structures / Irregular / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / DI(HYDROXYETHYL)ETHER / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsTan, K. / Bigelow, L. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase from Enterococcus faecalis V583.
Authors: Tan, K. / Bigelow, L. / Clancy, S. / Joachimiak, A.
History
DepositionMar 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 25, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase
B: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase
C: 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,18119
Polymers75,4573
Non-polymers72416
Water9,278515
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-47.4 kcal/mol
Surface area27690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.209, 55.179, 140.387
Angle α, β, γ (deg.)90.00, 95.63, 90.00
Int Tables number5
Space group name H-MC121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN AT THE TIME OF DEPOSITION, HOWEVER, FROM THE CRYSTAL STRUCTURE, THE THREE CHAINS A, B AND C LIKELY FORM A TRIMER.

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-acetyltransferase / Tetrahydrodipicolinate N-acetyltransferase / THP acetyltransferase / Tetrahydropicolinate acetylase


Mass: 25152.342 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: dapD, dapH, EF_1133 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q836H8, tetrahydrodipicolinate N-acetyltransferase

-
Non-polymers , 6 types, 531 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 515 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.9
Details: 0.2M MgCl2, 0.1M HEPES, 30% PEG 400, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97948 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.95→46 Å / Num. all: 51845 / Num. obs: 51845 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 13.8
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.563 / Mean I/σ(I) obs: 1.63 / Num. unique all: 2211 / % possible all: 83.9

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→45.83 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 7.509 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.178 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24845 2616 5 %RANDOM
Rwork0.20131 ---
all0.20364 49205 --
obs0.20364 49205 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.741 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20.06 Å2
2---0.02 Å20 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.95→45.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4810 0 39 515 5364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224915
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9726667
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2855659
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.84326.333180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.90315837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3531515
X-RAY DIFFRACTIONr_chiral_restr0.0890.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023588
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.22350
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23340
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2449
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7311.53363
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04925239
X-RAY DIFFRACTIONr_scbond_it1.98131727
X-RAY DIFFRACTIONr_scangle_it3.264.51425
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 165 -
Rwork0.267 3017 -
obs-3182 82.5 %
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)
111.14651.93339.26125.67341.531116.54150.16310.3158-0.17020.1244-0.0606-0.35310.16250.5612-0.1026-0.1798-0.02210.0541-0.2299-0.01570.0476-6.66724.66737.763
22.39-0.11690.18682.12571.34385.24260.05790.7470.3627-0.6739-0.01850.0271-0.122-0.1303-0.03940.0906-0.0035-0.01370.09750.104-0.1006-26.61615.88213.61
32.00180.1067-0.34911.51920.01743.27590.0134-0.1607-0.00860.081-0.0147-0.1933-0.00820.22590.0013-0.2323-0.0021-0.0278-0.17420.0051-0.1504-8.7486.27347.902
412.8980.1358-6.64825.2196.466617.9290.2875-0.20740.6077-0.4631-0.13420.1241-0.931-0.2579-0.1533-0.2250.0154-0.0103-0.16760.03660.0036-49.0578.01937.97
53.21890.0484-2.30931.388-0.16186.0131-0.090.8208-0.3422-0.5536-0.00010.12220.0884-0.30170.09020.048-0.0305-0.06720.1271-0.0947-0.0728-31.538-5.67713.63
61.6018-0.06180.20532.1659-0.11123.3235-0.0402-0.08440.18340.14320.01580.1049-0.123-0.13550.0244-0.21380.0296-0.0075-0.2113-0.0105-0.161-32.10714.35447.666
76.6932-4.0324-1.98319.0031-6.333118.1081-0.3270.1215-0.8924-0.26180.24120.46420.7703-0.62940.0857-0.1780.0051-0.0266-0.233-0.04340.0219-13.487-21.24938.144
83.1663-0.17640.59112.174-1.24176.0330.07180.93460.0114-0.6554-0.1787-0.17110.1840.18540.10680.05790.0390.05320.1531-0.0299-0.0876-10.320.81513.637
91.8020.09350.14711.56180.14113.63610.0212-0.0791-0.21070.152-0.04350.07640.1874-0.07270.0223-0.1925-0.01670.012-0.23060.0112-0.1499-27.482-9.72247.819
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 133 - 16
2X-RAY DIFFRACTION2AA14 - 7917 - 82
3X-RAY DIFFRACTION3AA80 - 21883 - 221
4X-RAY DIFFRACTION4BB-1 - 132 - 16
5X-RAY DIFFRACTION5BB14 - 7917 - 82
6X-RAY DIFFRACTION6BB80 - 21683 - 219
7X-RAY DIFFRACTION7CC-1 - 132 - 16
8X-RAY DIFFRACTION8CC14 - 7917 - 82
9X-RAY DIFFRACTION9CC80 - 21783 - 220

+
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