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- PDB-6a6e: Crystal structure of thermostable Cysteine desulfurase (FiSufS) f... -

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Basic information

Entry
Database: PDB / ID: 6a6e
TitleCrystal structure of thermostable Cysteine desulfurase (FiSufS) from thermophilic Fervidobacterium Islandicum AW-1
ComponentsCysteine desulfurase
KeywordsTRANSFERASE / Cysteine desulfurase / Thermophile / Suf gene cluster
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding
Similarity search - Function
Cysteine desulfurase, SufS / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / 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, SufS / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / DI(HYDROXYETHYL)ETHER / PYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase
Similarity search - Component
Biological speciesFervidobacterium islandicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsDhanasingh, I. / Jin, H.S. / Lee, D.W. / Lee, S.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
2014R1A2A2A01006765 Korea, Republic Of
2009-0064846 Korea, Republic Of
CitationJournal: Microb Biotechnol / Year: 2020
Title: The sulfur formation system mediating extracellular cysteine-cystine recycling in Fervidobacterium islandicum AW-1 is associated with keratin degradation.
Authors: Jin, H.S. / Dhanasingh, I. / Sung, J.Y. / La, J.W. / Lee, Y. / Lee, E.M. / Kang, Y. / Lee, D.Y. / Lee, S.H. / Lee, D.W.
History
DepositionJun 27, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / Item: _citation.title
Revision 1.2Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Nov 22, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine desulfurase
B: Cysteine desulfurase
C: Cysteine desulfurase
D: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,38338
Polymers190,5774
Non-polymers4,80634
Water22,0861226
1
A: Cysteine desulfurase
B: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,66920
Polymers95,2892
Non-polymers2,38018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12690 Å2
ΔGint-30 kcal/mol
Surface area27900 Å2
MethodPISA
2
C: Cysteine desulfurase
D: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,71418
Polymers95,2892
Non-polymers2,42616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12420 Å2
ΔGint-30 kcal/mol
Surface area27650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.302, 218.716, 89.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Cysteine desulfurase / SufS


Mass: 47644.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fervidobacterium islandicum (bacteria) / Gene: NA23_08315 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1B0VPZ3, cysteine desulfurase

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Non-polymers , 5 types, 1260 molecules

#2: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H8O7
#5: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1226 / 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: 2.73 Å3/Da / Density % sol: 55.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2M diAmmonium hydrogen citrate, 20% PEG 3350, pH 5.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.095→26.755 Å / Num. obs: 122276 / % possible obs: 98.68 % / Redundancy: 12.3 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 26.84
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.524

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T3I

1t3i


Resolution: 2.09→26.755 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.59 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18685 6103 5 %RANDOM
Rwork0.14162 ---
obs0.14387 115598 98.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.234 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.09→26.755 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13360 0 314 1226 14900
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01913946
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213017
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.97518832
X-RAY DIFFRACTIONr_angle_other_deg0.896330245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.53551688
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5624.653606
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.803152416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4691548
X-RAY DIFFRACTIONr_chiral_restr0.1090.22137
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215170
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022722
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_it2.1672.3776752
X-RAY DIFFRACTIONr_mcbond_other2.1622.3766751
X-RAY DIFFRACTIONr_mcangle_it3.0263.558434
X-RAY DIFFRACTIONr_mcangle_other3.0263.558435
X-RAY DIFFRACTIONr_scbond_it3.7392.9567193
X-RAY DIFFRACTIONr_scbond_other3.7362.9567193
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6914.21610397
X-RAY DIFFRACTIONr_long_range_B_refined7.86330.8816282
X-RAY DIFFRACTIONr_long_range_B_other7.86530.88316283
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.095→2.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 405 -
Rwork0.185 7427 -
obs--86.69 %

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