[English] 日本語
Yorodumi
- PDB-3r5d: Pseudomonas aeruginosa DapD (PA3666) apoprotein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3r5d
TitlePseudomonas aeruginosa DapD (PA3666) apoprotein
ComponentsTetrahydrodipicolinate N-succinyletransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase activity / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / magnesium ion binding / cytoplasm
Similarity search - Function
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, gammaproteobacteria / Tetrahydrodipicolinate N-succinyltransferase N-terminal / Trimeric LpxA-like enzymes / Alpha-Beta Plaits - #2010 / Type 2 tetrahydrodipicolinate N-succinyltransferase family / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain superfamily / Tetrahydrodipicolinate N-succinyltransferase middle / Hexapeptide repeat of succinyl-transferase / Wheat Germ Agglutinin (Isolectin 2); domain 1 ...2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, gammaproteobacteria / Tetrahydrodipicolinate N-succinyltransferase N-terminal / Trimeric LpxA-like enzymes / Alpha-Beta Plaits - #2010 / Type 2 tetrahydrodipicolinate N-succinyltransferase family / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain superfamily / Tetrahydrodipicolinate N-succinyltransferase middle / Hexapeptide repeat of succinyl-transferase / Wheat Germ Agglutinin (Isolectin 2); domain 1 / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Trimeric LpxA-like superfamily / 3 Solenoid / Alpha-Beta Plaits / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase / 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSandalova, T. / Schnell, R. / Schneider, G.
CitationJournal: Plos One / Year: 2012
Title: Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion.
Authors: Schnell, R. / Oehlmann, W. / Sandalova, T. / Braun, Y. / Huck, C. / Maringer, M. / Singh, M. / Schneider, G.
History
DepositionMar 18, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2012Group: Structure summary
Revision 1.2Mar 30, 2016Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tetrahydrodipicolinate N-succinyletransferase
B: Tetrahydrodipicolinate N-succinyletransferase
C: Tetrahydrodipicolinate N-succinyletransferase
D: Tetrahydrodipicolinate N-succinyletransferase
E: Tetrahydrodipicolinate N-succinyletransferase
F: Tetrahydrodipicolinate N-succinyletransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,9148
Polymers217,7306
Non-polymers1842
Water12,701705
1
A: Tetrahydrodipicolinate N-succinyletransferase
B: Tetrahydrodipicolinate N-succinyletransferase
C: Tetrahydrodipicolinate N-succinyletransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9574
Polymers108,8653
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9510 Å2
ΔGint-17 kcal/mol
Surface area34980 Å2
MethodPISA
2
D: Tetrahydrodipicolinate N-succinyletransferase
E: Tetrahydrodipicolinate N-succinyletransferase
F: Tetrahydrodipicolinate N-succinyletransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9574
Polymers108,8653
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9540 Å2
ΔGint-17 kcal/mol
Surface area34640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.038, 102.002, 134.903
Angle α, β, γ (deg.)90.00, 89.97, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
12D
22E
32F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 329
2114B1 - 329
3114C1 - 329
1124D1 - 329
2124E1 - 329
3124F1 - 329

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Tetrahydrodipicolinate N-succinyletransferase / Tetrahydrodipicolinate succinylase


Mass: 36288.379 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: dapD, PA3666 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9Z9H2, UniProt: G3XD76*PLUS, 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 19-20% of PEG3350, 0.3-0.4M succinate, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 7, 2009
RadiationMonochromator: Si (111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.507
11h,-k,-l20.493
ReflectionResolution: 1.8→25.06 Å / Num. all: 190821 / Num. obs: 190821 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 10.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.8 / Rsym value: 0.37 / % possible all: 62.7

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R5C

3r5c


Resolution: 1.8→24.38 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.919 / SU B: 2.458 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.028 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23639 9659 5.1 %RANDOM
Rwork0.20156 ---
obs0.20332 181087 91.61 %-
all-181087 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.338 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å2-0.5 Å2
2---0.19 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→24.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14144 0 12 705 14861
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02214424
X-RAY DIFFRACTIONr_bond_other_d0.0010.029489
X-RAY DIFFRACTIONr_angle_refined_deg1.0861.9819587
X-RAY DIFFRACTIONr_angle_other_deg0.838323331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.77251921
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.48324.698547
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.951152358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8591573
X-RAY DIFFRACTIONr_chiral_restr0.0610.22335
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02116202
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022731
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3681.59482
X-RAY DIFFRACTIONr_mcbond_other0.1091.53967
X-RAY DIFFRACTIONr_mcangle_it0.654215082
X-RAY DIFFRACTIONr_scbond_it0.92534942
X-RAY DIFFRACTIONr_scangle_it1.4684.54495
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3926medium positional0.250.5
11B3926medium positional0.230.5
11C3926medium positional0.250.5
22D3913medium positional0.260.5
22E3913medium positional0.230.5
22F3913medium positional0.260.5
11A3926medium thermal0.332
11B3926medium thermal0.512
11C3926medium thermal0.612
22D3913medium thermal0.372
22E3913medium thermal0.552
22F3913medium thermal0.642
LS refinement shellResolution: 1.799→1.845 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 440 -
Rwork0.278 8136 -
obs--56.15 %

+
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://pdbjlvh1.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