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- PDB-1eg5: NIFS-LIKE PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1eg5
TitleNIFS-LIKE PROTEIN
ComponentsAMINOTRANSFERASE
KeywordsTRANSFERASE / PLP-DEPENDENT ENZYMES / IRON-SULFUR-CLUSTER SYNTHESIS / C-S BETA LYASE
Function / homology
Function and homology information


cysteine desulfurase / nitrogen fixation / transaminase activity
Similarity search - Function
Cysteine desulfurase / Aminotransferase class V domain / Aminotransferase class-V / 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 ...Cysteine desulfurase / Aminotransferase class V domain / Aminotransferase class-V / 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
PYRIDOXAL-5'-PHOSPHATE / cysteine desulfurase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsKaiser, J.T. / Clausen, T. / Bourenkow, G.P. / Bartunik, H.-D. / Steinbacher, S. / Huber, R.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Crystal structure of a NifS-like protein from Thermotoga maritima: implications for iron sulphur cluster assembly.
Authors: Kaiser, J.T. / Clausen, T. / Bourenkow, G.P. / Bartunik, H.D. / Steinbacher, S. / Huber, R.
History
DepositionFeb 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AMINOTRANSFERASE
B: AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5816
Polymers86,8952
Non-polymers6864
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6300 Å2
ΔGint-62 kcal/mol
Surface area26950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.110, 114.110, 156.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein AMINOTRANSFERASE


Mass: 43447.375 Da / Num. of mol.: 2
Mutation: M1(MSE),M21(MSE),M38(MSE),M46(MSE),M106(MSE),M111(MSE),M146(MSE),M251(MSE),M265(MSE),M277(MSE),M338(MSE)
Source method: isolated from a genetically manipulated source
Details: NIFS-LIKE PROTEIN / Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: ORF 1692 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X218
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 3.39 Å3/Da / Density % sol: 63.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: ammonium sulphate, hepes, dtt, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 18K
Crystal grow
*PLUS
pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-20 mg/mlprotein1drop
210 mMdithiothreitol1drop
30.9 Mammonium sulfate1reservoir
4100 mMNaOH/HEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.25 / Wavelength: 1.25, 0.977250, 0.976430
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 1, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.251
20.977251
30.976431
ReflectionResolution: 2→500 Å / Num. all: 80240 / Num. obs: 78802 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.054
Reflection shellResolution: 2→2.13 Å / Num. unique all: 12186 / % possible all: 97.1
Reflection
*PLUS
Num. obs: 80563 / % possible obs: 95.7 % / Num. measured all: 233681 / Rmerge(I) obs: 0.081

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Processing

Software
NameVersionClassification
SHARPphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2→35.92 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3535820.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENG&HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3930 5 %RANDOM
Rwork0.211 ---
all0.211 81155 --
obs0.211 78802 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.07 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 38.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.45 Å25.14 Å20 Å2
2--3.45 Å20 Å2
3----6.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2→35.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5717 0 40 255 6012
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.8
X-RAY DIFFRACTIONc_mcbond_it2.912
X-RAY DIFFRACTIONc_mcangle_it3.742.5
X-RAY DIFFRACTIONc_scbond_it4.832.5
X-RAY DIFFRACTIONc_scangle_it6.533
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 635 5 %
Rwork0.34 12186 -
obs--97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PLP.CNS.PARPLP.CNS.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 38.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.8
X-RAY DIFFRACTIONc_mcbond_it2
X-RAY DIFFRACTIONc_scbond_it2.5
X-RAY DIFFRACTIONc_mcangle_it2.5
X-RAY DIFFRACTIONc_scangle_it3
LS refinement shell
*PLUS
Rfactor Rfree: 0.354 / % reflection Rfree: 5 % / Rfactor Rwork: 0.34

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