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- PDB-1t3i: Structure of slr0077/SufS, the Essential Cysteine Desulfurase fro... -

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Basic information

Entry
Database: PDB / ID: 1t3i
TitleStructure of slr0077/SufS, the Essential Cysteine Desulfurase from Synechocystis PCC 6803
ComponentsProbable cysteine desulfurase
KeywordsTRANSFERASE / PLP-binding enzyme / cysteine desulfurase
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding
Similarity search - Function
Cysteine desulfurase, SufS / 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, SufS / 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
octanoyl-sucrose, esterificated at glucose C3 / PYRIDOXAL-5'-PHOSPHATE / Probable cysteine desulfurase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsTirupati, B. / Vey, J.L. / Drennan, C.L. / Bollinger Jr., J.M.
CitationJournal: Biochemistry / Year: 2004
Title: Kinetic and structural characterization of Slr0077/SufS, the essential cysteine desulfurase from Synechocystis sp. PCC 6803.
Authors: Tirupati, B. / Vey, J.L. / Drennan, C.L. / Bollinger Jr., J.M.
History
DepositionApr 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.pdbx_description / _entity.type
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable cysteine desulfurase
B: Probable cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0707
Polymers92,9232
Non-polymers1,1475
Water10,323573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9180 Å2
ΔGint-41 kcal/mol
Surface area25630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.386, 89.308, 141.815
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains the full biological assembly (protein is a homodimer).

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Components

#1: Protein Probable cysteine desulfurase


Mass: 46461.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Gene: CSD, SLR0077 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) star cells / References: UniProt: Q55793, cysteine desulfurase
#2: Polysaccharide beta-D-fructofuranose-(2-1)-3-O-octanoyl-alpha-D-glucopyranose / octanoyl-sucrose / esterificated at glucose C3


Type: oligosaccharide, Oligosaccharide / Class: Substrate analog / Mass: 468.493 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with reducing-end-to-reducing-end glycosidic bond
References: octanoyl-sucrose, esterificated at glucose C3
DescriptorTypeProgram
WURCS=2.0/2,2,1/[ha122h-2b_2-5][a2122h-1a_1-5_3*OCCCCCCCC/3=O]/1-2/a2-b1WURCSPDB2Glycan 1.1.0
[][b-D-Fruf]{t;]{[(2+1)][a-D-Glcp]{[(3+1)][<C8O1>]{}}}LINUCSPDB-CARE
#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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / 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: 2.98 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M tris pH 8.0, 0.25M MgCl2, 25% PEG 4000, n-octanoylsucrose, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2002
RadiationMonochromator: Double crystal, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.79→42.59 Å / Num. all: 104503 / Num. obs: 94984 / % possible obs: 90.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4 % / Biso Wilson estimate: 25.9 Å2 / Limit h max: 47 / Limit h min: 0 / Limit k max: 48 / Limit k min: 0 / Limit l max: 78 / Limit l min: 0 / Observed criterion F max: 298662.48 / Observed criterion F min: 0.32 / Rsym value: 0.062 / Net I/σ(I): 18.1
Reflection shellResolution: 1.8→1.98 Å / Mean I/σ(I) obs: 4.5 / Rsym value: 0.324 / % possible all: 83.3

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Processing

Software
NameVersionClassificationNB
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: polyalanine version of 1JF9.pdb

1jf9


Resolution: 1.8→42.59 Å / Rfactor Rfree error: 0.002 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.216 9531 10 %RANDOM
Rwork0.191 ---
obs0.194 94984 90.9 %-
all-104466 --
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 47.2305 Å2 / ksol: 0.357404 e/Å3
Displacement parametersBiso max: 65.35 Å2 / Biso mean: 28.36 Å2 / Biso min: 17.67 Å2
Baniso -1Baniso -2Baniso -3
1--3.411 Å20 Å20 Å2
2---7.776 Å20 Å2
3---11.187 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Luzzati d res high-1.8
Refinement stepCycle: LAST / Resolution: 1.8→42.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6211 0 74 573 6858
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_mcbond_it1.0581.5
X-RAY DIFFRACTIONc_mcangle_it1.5332
X-RAY DIFFRACTIONc_scbond_it1.8672
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.8-1.880.2779827.60.28186380.00912924962074.4
1.88-1.980.23410458.10.23697230.007129281076883.3
1.98-2.110.21412079.30.213103510.006129821155889
2.11-2.270.19712059.30.195107940.006129601199992.6
2.27-2.50.19412189.30.193110510.006130301226994.2
2.5-2.860.19612179.30.196113340.006130601255196.1
2.86-3.60.19512839.80.193115710.005131471285497.8
3.6-42.590.181137410.10.182119910.005135451336598.7
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3prost.parprost.top
X-RAY DIFFRACTION4water.paramwater.top

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