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- PDB-7tlp: Structure of Atopobium parvulum SufS K235R -

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Basic information

Entry
Database: PDB / ID: 7tlp
TitleStructure of Atopobium parvulum SufS K235R
ComponentsCysteine desulfurase
KeywordsTRANSFERASE / Cysteine desulferase
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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-PLG / Cysteine desulfurase
Similarity search - Component
Biological speciesLancefieldella parvula (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsKarunakaran, G. / Couture, J.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Febs Lett. / Year: 2022
Title: Structural analysis of Atopobium parvulum SufS cysteine desulfurase linked to Crohn's disease.
Authors: Karunakaran, G. / Yang, Y. / Tremblay, V. / Ning, Z. / Martin, J. / Belaouad, A. / Figeys, D. / Brunzelle, J.S. / Giguere, P.M. / Stintzi, A. / Couture, J.F.
History
DepositionJan 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
E: Cysteine desulfurase
F: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)296,87412
Polymers295,0376
Non-polymers1,8376
Water00
1
A: Cysteine desulfurase
hetero molecules

A: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9584
Polymers98,3462
Non-polymers6122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area3550 Å2
ΔGint-20 kcal/mol
Surface area26620 Å2
MethodPISA
2
B: Cysteine desulfurase
hetero molecules

D: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9584
Polymers98,3462
Non-polymers6122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555x+1/2,y+1/2,z1
Buried area3880 Å2
ΔGint-25 kcal/mol
Surface area26590 Å2
MethodPISA
3
C: Cysteine desulfurase
E: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9584
Polymers98,3462
Non-polymers6122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-20 kcal/mol
Surface area26500 Å2
MethodPISA
4
F: Cysteine desulfurase
hetero molecules

F: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9584
Polymers98,3462
Non-polymers6122
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4100 Å2
ΔGint-26 kcal/mol
Surface area26350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.744, 159.262, 178.069
Angle α, β, γ (deg.)90.000, 90.155, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and ((resid 1 through 11 and (name N...
d_2ens_1(chain "B" and ((resid 1 through 11 and (name N...
d_3ens_1(chain "C" and ((resid 1 through 11 and (name N...
d_4ens_1(chain "D" and ((resid 1 through 11 and (name N...
d_5ens_1(chain "E" and ((resid 1 through 11 and (name N...
d_6ens_1(chain "F" and ((resid 1 through 11 and (name N...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg label comp-IDEnd label comp-IDLabel asym-IDLabel seq-ID
d_11ens_1METASPA1 - 31
d_12ens_1ALAGLNA35 - 48
d_13ens_1ARGSERA50 - 100
d_14ens_1LEUALAA104 - 157
d_15ens_1LYSVALA161 - 348
d_16ens_1ILEPHEA350 - 397
d_17ens_1LIGLIGB
d_21ens_1METASPC1 - 31
d_22ens_1ALAGLNC35 - 48
d_23ens_1ARGASNC52 - 58
d_24ens_1ASPSERC61 - 104
d_25ens_1LEUALAC106 - 159
d_26ens_1LYSVALC163 - 350
d_27ens_1ILEPHEC352 - 399
d_28ens_1LIGLIGD
d_31ens_1METASPE1 - 31
d_32ens_1ALAGLNE33 - 46
d_33ens_1ARGASNE48 - 54
d_34ens_1ASPSERE56 - 99
d_35ens_1LEUALAE103 - 156
d_36ens_1LYSVALE160 - 347
d_37ens_1ILEPHEE351 - 398
d_38ens_1LIGLIGF
d_41ens_1METASPG1 - 31
d_42ens_1ALAGLNG33 - 46
d_43ens_1ARGASNG50 - 56
d_44ens_1ASPSERG63 - 106
d_45ens_1LEUALAG110 - 163
d_46ens_1LYSMETG167 - 262
d_47ens_1ALAVALG264 - 355
d_48ens_1ILEPHEG357 - 404
d_49ens_1LIGLIGH
d_51ens_1METASPI1 - 31
d_52ens_1ALAGLNI33 - 46
d_53ens_1ARGASNI48 - 54
d_54ens_1ASPSERI58 - 101
d_55ens_1LEUALAI105 - 158
d_56ens_1LYSMETI162 - 257
d_57ens_1ALAVALI259 - 350
d_58ens_1ILEPHEI352 - 399
d_59ens_1LIGLIGJ
d_61ens_1METASPK1 - 31
d_62ens_1ALAGLNK33 - 46
d_63ens_1ARGASNK50 - 56
d_64ens_1ASPSERK61 - 104
d_65ens_1LEUALAK108 - 161
d_66ens_1LYSMETK163 - 258
d_67ens_1ALAVALK260 - 351
d_68ens_1ILEPHEK355 - 402
d_69ens_1LIGLIGL

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Components

#1: Protein
Cysteine desulfurase


Mass: 49172.844 Da / Num. of mol.: 6 / Mutation: K235R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lancefieldella parvula (bacteria) / Gene: Apar_0399 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C8W9P2, cysteine desulfurase
#2: Chemical
ChemComp-PLG / N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] / N-PYRIDOXYL-GLYCINE-5-MONOPHOSPHATE


Mass: 306.209 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N2O7P / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 2.31 Å3/Da / Density % sol: 46.65 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 10% PEG8000, 12% ethylene glycol, 50 mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.99→38.88 Å / Num. obs: 49721 / % possible obs: 96.4 % / Redundancy: 4.11 % / Biso Wilson estimate: 68.77 Å2 / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.084 / Χ2: 1.06 / Net I/σ(I): 12.3 / Num. measured all: 232254 / Scaling rejects: 27871
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRrim(I) allΧ2Rejects% possible all
2.99-3.14.090.2265.12138147830.2581.17183893.3
3.1-3.224.260.2065.82341249510.2341.18230396.5
3.22-3.374.170.1676.82346549730.1911.17271096.4
3.37-3.554.150.1337.92351649940.1521.11276696.8
3.55-3.774.120.099112332349430.1121.07294596.8
3.77-4.064.160.079132350650050.0911.02267997.1
4.06-4.474.160.06615.52332549760.0750.97264297.2
4.47-5.114.140.05718.12384951010.0660.93275597.5
5.11-6.444.120.05917.42340750260.0670.96269997.7
6.44-38.883.730.04422.82307049690.0510.98453494.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
d*TREK9.9.9.11W9Rdata scaling
PDB_EXTRACT3.27data extraction
d*TREKdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J8Q

5j8q


Resolution: 2.99→38.86 Å / SU ML: 0.5115 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.2599
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3088 2005 4.04 %
Rwork0.237 47636 -
obs0.2399 49641 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.42 Å2
Refinement stepCycle: LAST / Resolution: 2.99→38.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16502 0 120 0 16622
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011717007
X-RAY DIFFRACTIONf_angle_d1.334523347
X-RAY DIFFRACTIONf_chiral_restr0.07752810
X-RAY DIFFRACTIONf_plane_restr0.00843050
X-RAY DIFFRACTIONf_dihedral_angle_d9.68822558
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.437931302703
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.448787876812
ens_1d_4AX-RAY DIFFRACTIONTorsion NCS0.378074347052
ens_1d_5AX-RAY DIFFRACTIONTorsion NCS0.419210756416
ens_1d_6AX-RAY DIFFRACTIONTorsion NCS0.405846194902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.070.35341410.2553284X-RAY DIFFRACTION92.19
3.07-3.150.29021450.26423353X-RAY DIFFRACTION96.39
3.15-3.240.39221490.27573428X-RAY DIFFRACTION96.49
3.24-3.350.40731400.30243335X-RAY DIFFRACTION96.26
3.35-3.470.4091480.29833411X-RAY DIFFRACTION96.66
3.47-3.610.44131400.26833403X-RAY DIFFRACTION96.75
3.61-3.770.2821490.24033410X-RAY DIFFRACTION96.84
3.77-3.970.28661450.24153441X-RAY DIFFRACTION97.05
3.97-4.220.41521440.21823408X-RAY DIFFRACTION97.16
4.22-4.540.2691470.20673466X-RAY DIFFRACTION97.31
4.54-50.29661480.213412X-RAY DIFFRACTION97.43
5-5.720.30191360.23833501X-RAY DIFFRACTION97.61
5.72-7.20.25521420.25833451X-RAY DIFFRACTION97.69
7.2-38.860.23641310.20393333X-RAY DIFFRACTION91.98
Refinement TLS params.Method: refined / Origin x: -28.2574402091 Å / Origin y: -51.0366307915 Å / Origin z: 43.8093505515 Å
111213212223313233
T0.620818729358 Å20.00391731201402 Å2-0.011992686601 Å2-0.611049387855 Å20.0248814300674 Å2--0.622353565625 Å2
L0.0661466968651 °20.00754326392552 °20.0237369711162 °2-0.0277295043848 °20.0456658477943 °2--0.148018428339 °2
S-0.0140265271135 Å °-0.0133046773942 Å °0.0104973404898 Å °-0.000482823347415 Å °0.000681016766625 Å °0.0166665403486 Å °0.0030825820548 Å °0.0189716000866 Å °0.0112220281759 Å °
Refinement TLS groupSelection details: all

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