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- PDB-2dou: probable N-succinyldiaminopimelate aminotransferase (TTHA0342) fr... -

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Basic information

Entry
Database: PDB / ID: 2dou
Titleprobable N-succinyldiaminopimelate aminotransferase (TTHA0342) from Thermus thermophilus HB8
Componentsprobable N-succinyldiaminopimelate aminotransferase
KeywordsTRANSFERASE / PLP-dependent enzyme / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Transferases; Transferring nitrogenous groups; Transaminases / transaminase activity / biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
: / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...: / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsOmi, R. / Goto, M. / Miyahara, I. / Hirotsu, K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: probable N-succinyldiaminopimelate aminotransferase (TTHA0342) from Thermus thermophilus HB8
Authors: Omi, R. / Goto, M. / Miyahara, I. / Hirotsu, K.
History
DepositionMay 3, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: probable N-succinyldiaminopimelate aminotransferase
B: probable N-succinyldiaminopimelate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1787
Polymers82,5552
Non-polymers6235
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-88 kcal/mol
Surface area25970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.490, 121.490, 172.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein probable N-succinyldiaminopimelate aminotransferase


Mass: 41277.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SLF1, Transferases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 3.85 Å3/Da / Density % sol: 68.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulfate, PEG 8000, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 1109831 / % possible obs: 100 % / Biso Wilson estimate: 25.9 Å2

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCdata collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→19.98 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2778754.58 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.254 5791 10 %RANDOM
Rwork0.222 ---
obs0.222 57630 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.731 Å2 / ksol: 0.361433 e/Å3
Displacement parametersBiso mean: 37.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.38 Å20 Å20 Å2
2--4.38 Å20 Å2
3----8.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5582 0 35 204 5821
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_mcbond_it1.061.5
X-RAY DIFFRACTIONc_mcangle_it1.652
X-RAY DIFFRACTIONc_scbond_it24.42
X-RAY DIFFRACTIONc_scangle_it22.162.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 945 10.1 %
Rwork0.259 8422 -
obs--99 %

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