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- PDB-1ecx: NIFS-LIKE PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1ecx
TitleNIFS-LIKE PROTEIN
ComponentsAMINOTRANSFERASE
KeywordsTRANSFERASE / plp-dependent enzymes / iron-sulfur-cluster synthesis / c-s beta lyase
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / transaminase activity / iron-sulfur cluster binding / metal ion binding
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
CYSTEINE / PYRIDOXAL-5'-PHOSPHATE / cysteine desulfurase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.7 Å
AuthorsKaiser, J.T. / Clausen, T.C. / 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
DepositionJan 26, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Experimental preparation / Category: exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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

Downloads & links

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Assembly

Deposited unit
A: AMINOTRANSFERASE
B: AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6006
Polymers85,8632
Non-polymers7374
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: AMINOTRANSFERASE
hetero molecules

B: AMINOTRANSFERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6006
Polymers85,8632
Non-polymers7374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+1,-x+y,-z+1/31
Buried area6060 Å2
ΔGint-25 kcal/mol
Surface area27120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.410, 115.410, 156.950
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: 42931.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: NIFS-LIKE PROTEIN / Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X218
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 3.51 Å3/Da / Density % sol: 64.99 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: AMMONIUMSULPHATE, 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 (eV)
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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→34.04 Å / Num. all: 33763 / Num. obs: 33510 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.102
Reflection shellResolution: 2.7→2.87 Å / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 2.7→34.04 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2258073.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1661 5 %RANDOM
Rwork0.207 ---
obs0.207 33510 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.29 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso mean: 36.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å25.39 Å20 Å2
2--3.27 Å20 Å2
3----6.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.7→34.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5717 0 42 179 5938
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_mcbond_it1.141.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it1.72
X-RAY DIFFRACTIONc_scangle_it2.562.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 270 4.9 %
Rwork0.284 5215 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PLP.CNS.PARAMPLP.CNS.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.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: 36.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.07
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.334 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.284

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