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- PDB-3dwm: Crystal structure of Mycobacterium tuberculosis CysO, an antigen -

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Basic information

Entry
Database: PDB / ID: 3dwm
TitleCrystal structure of Mycobacterium tuberculosis CysO, an antigen
Components9.5 kDa culture filtrate antigen cfp10A
KeywordsTRANSFERASE / Ubiquitin like / Sulfur carrier protein
Function / homology
Function and homology information


Cysteine synthesis from O-phosphoserine / cysteine biosynthetic process / protein-containing complex / cytosol
Similarity search - Function
: / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Sulfur carrier protein CysO / Sulfur carrier protein CysO
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsJurgenson, C.T. / Burns, K.E. / Begley, T.P. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2008
Title: Crystal structure of a sulfur carrier protein complex found in the cysteine biosynthetic pathway of Mycobacterium tuberculosis.
Authors: Jurgenson, C.T. / Burns, K.E. / Begley, T.P. / Ealick, S.E.
History
DepositionJul 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 9.5 kDa culture filtrate antigen cfp10A
B: 9.5 kDa culture filtrate antigen cfp10A


Theoretical massNumber of molelcules
Total (without water)19,1292
Polymers19,1292
Non-polymers00
Water43224
1
A: 9.5 kDa culture filtrate antigen cfp10A


Theoretical massNumber of molelcules
Total (without water)9,5651
Polymers9,5651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 9.5 kDa culture filtrate antigen cfp10A


Theoretical massNumber of molelcules
Total (without water)9,5651
Polymers9,5651
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.934, 62.988, 36.537
Angle α, β, γ (deg.)90.00, 114.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-102-

HOH

21B-105-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Refine code: 2

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALGLNGLNAA3 - 183 - 18
21VALVALGLNGLNBB3 - 183 - 18
12SERSERSERSERAA20 - 4320 - 43
22SERSERSERSERBB20 - 4320 - 43
13ARGARGALAALAAA45 - 8945 - 89
23ARGARGALAALABB45 - 8945 - 89

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Components

#1: Protein 9.5 kDa culture filtrate antigen cfp10A


Mass: 9564.656 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: cfp10A, Rv1335, MT1376.1, MTCY130.20 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A646, UniProt: P9WP33*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M NaNO3, 20% w/v PEG 3350, plus Rv3206 in a 1:1 mass ratio, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 14, 2007
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.69→39.97 Å / Num. obs: 5022 / % possible obs: 99.2 % / Redundancy: 4 % / Rsym value: 0.145 / Net I/σ(I): 14.5
Reflection shellResolution: 2.69→2.76 Å / Redundancy: 3 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.392 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0026refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DWG, chain C

3dwg


Resolution: 2.69→39.97 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.909 / SU B: 13.295 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25162 231 4.6 %RANDOM
Rwork0.19542 ---
obs0.19785 4791 98.18 %-
all-5022 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.931 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0.5 Å2
2--0.09 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 2.69→39.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1264 0 0 24 1288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221286
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.971760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.515176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.81423.77845
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.37115181
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.298158
X-RAY DIFFRACTIONr_chiral_restr0.1210.2217
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02976
X-RAY DIFFRACTIONr_nbd_refined0.2480.2606
X-RAY DIFFRACTIONr_nbtor_refined0.3230.2882
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.248
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.232
X-RAY DIFFRACTIONr_mcbond_it0.7061.5892
X-RAY DIFFRACTIONr_mcangle_it1.23621416
X-RAY DIFFRACTIONr_scbond_it1.8953420
X-RAY DIFFRACTIONr_scangle_it3.0184.5344
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A340tight positional0.030.05
B267medium positional0.040.5
A340tight thermal0.070.5
B267medium thermal0.12
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.479 16 -
Rwork0.284 271 -
obs--79.94 %

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