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- PDB-4hvk: Crystal structure and functional studies of an unusual L-cysteine... -

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Basic information

Entry
Database: PDB / ID: 4hvk
TitleCrystal structure and functional studies of an unusual L-cysteine desulfurase from Archaeoglobus fulgidus.
ComponentsProbable cysteine desulfurase 2
KeywordsTRANSFERASE / Transferase and IscS
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / [2Fe-2S] cluster assembly / 2 iron, 2 sulfur cluster binding / pyridoxal phosphate binding / metal ion binding / cytoplasm
Similarity search - Function
Cysteine desulfurase IscS / 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 ...Cysteine desulfurase IscS / 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
4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase IscS 2
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 Å
AuthorsYamanaka, Y. / Zeppieri, L. / Nicolet, Y. / Marinoni, E.N. / de Oliveira, J.S. / Masafumi, O. / Dean, D.R. / Fontecilla-Camps, J.C.
CitationJournal: Dalton Trans / Year: 2013
Title: Crystal structure and functional studies of an unusual L-cysteine desulfurase from Archaeoglobus fulgidus.
Authors: Yamanaka, Y. / Zeppieri, L. / Nicolet, Y. / Marinoni, E.N. / de Oliveira, J.S. / Odaka, M. / Dean, D.R. / Fontecilla-Camps, J.C.
History
DepositionNov 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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 cysteine desulfurase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,19515
Polymers41,8891
Non-polymers2,30614
Water6,828379
1
A: Probable cysteine desulfurase 2
hetero molecules

A: Probable cysteine desulfurase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,38930
Polymers83,7772
Non-polymers4,61228
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area11750 Å2
ΔGint-57 kcal/mol
Surface area26890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.060, 99.270, 108.860
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Probable cysteine desulfurase 2


Mass: 41888.582 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea)
Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126
Gene: AF0564, AF_0564, iscS2 / Production host: Escherichia coli (E. coli) / Strain (production host): C41 / References: UniProt: O29689, cysteine desulfurase

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Non-polymers , 5 types, 393 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N2O5P
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 379 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsAUTHORS STATE THAT THE CORRECTNESS OF THE SIDE CHAIN COULD BE DETERMINED BY INSPECTING THE ELECTRON DENSITY

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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: 2.26 Å3/Da / Density % sol: 45.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 200 mM Calcium acetate; 100 mM Sodium cacodylate; 40% PEG 300 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 5, 2009
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1.43→57 Å / Num. all: 70218 / Num. obs: 70218 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.43→1.47 Å / % possible all: 84.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→57 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.752 / SU ML: 0.031 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.052 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15067 3477 5 %RANDOM
Rwork0.1083 ---
all0.1104 70218 --
obs0.11042 65502 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.134 Å2
Baniso -1Baniso -2Baniso -3
1--0.92 Å20 Å20 Å2
2--1.33 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.43→57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2794 0 101 379 3274
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0193253
X-RAY DIFFRACTIONr_bond_other_d0.0020.022224
X-RAY DIFFRACTIONr_angle_refined_deg2.2251.994412
X-RAY DIFFRACTIONr_angle_other_deg1.17235496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3935434
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83124.855138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.62415568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8061523
X-RAY DIFFRACTIONr_chiral_restr0.1420.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023683
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02613
X-RAY DIFFRACTIONr_rigid_bond_restr6.99635470
X-RAY DIFFRACTIONr_sphericity_free32.553587
X-RAY DIFFRACTIONr_sphericity_bonded10.85555700
LS refinement shellResolution: 1.43→1.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.22 210 -
Rwork0.16 3923 -
obs--83.43 %

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