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- PDB-3dwg: Crystal structure of a sulfur carrier protein complex found in th... -

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Basic information

Entry
Database: PDB / ID: 3dwg
TitleCrystal structure of a sulfur carrier protein complex found in the cysteine biosynthetic pathway of Mycobacterium tuberculosis
Components
  • 9.5 kDa culture filtrate antigen cfp10A
  • Cysteine synthase B
KeywordsTRANSFERASE / Sulfur carrier protein complex / beta-grasp fold / Amino-acid biosynthesis / Cysteine biosynthesis / Pyridoxal phosphate
Function / homology
Function and homology information


[CysO sulfur-carrier protein]-thiocarboxylate-dependent cysteine synthase / Cysteine synthesis from O-phosphoserine / O-phosphoserine sulfhydrylase activity / cysteine biosynthetic process / cysteine synthase activity / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / pyridoxal phosphate binding / protein-containing complex / cytosol / cytoplasm
Similarity search - Function
Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Rossmann fold - #1100 / Beta-grasp domain / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme ...Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Rossmann fold - #1100 / Beta-grasp domain / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Sulfur carrier protein CysO / O-phosphoserine sulfhydrylase / Sulfur carrier protein CysO / O-phosphoserine sulfhydrylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.53 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine synthase B
B: Cysteine synthase B
C: 9.5 kDa culture filtrate antigen cfp10A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,5935
Polymers79,0993
Non-polymers4942
Water17,745985
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-31.6 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.810, 80.426, 89.619
Angle α, β, γ (deg.)90.00, 105.74, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains the biological unit consisting of two CysM protomers and one CysO protomer.

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Components

#1: Protein Cysteine synthase B / O-acetylserine sulfhydrylase B / O-acetylserine(Thiol)-lyase B / CSase B


Mass: 34767.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: cysM, Rv1336, MT1377, MTCY130.21 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)B834
References: UniProt: P63873, UniProt: P9WP53*PLUS, cysteine synthase
#2: Protein 9.5 kDa culture filtrate antigen cfp10A


Mass: 9564.656 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate / Pyridoxal phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 985 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.74 %
Crystal growTemperature: 295 K / pH: 5.8
Details: 7-10% w/v PEG 4000, 0.1 M Sodium citrate pH 5.8, 0.2 M Ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 295K, pH 5.80

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 24-ID-C10.9795
SYNCHROTRONAPS 8-BM20.9795
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDAug 22, 2005
ADSC QUANTUM 3152CCDAug 22, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(220)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 105098 / % possible obs: 96.3 % / Redundancy: 3.18 % / Rsym value: 0.046 / Net I/σ(I): 26.2
Reflection shellResolution: 1.53→1.57 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 4 / Rsym value: 0.219 / % possible all: 81.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.53→27.13 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.481 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.085 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.217 5513 5 %RANDOM
Rwork0.176 ---
obs0.178 105098 96.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.69 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.53→27.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5425 0 30 985 6440
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0225590
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8991.9737632
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5595746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.25923.258221
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6715838
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0661544
X-RAY DIFFRACTIONr_chiral_restr0.1310.2881
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024268
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.23020
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.23865
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2847
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.285
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2160.268
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3331.53731
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.94125803
X-RAY DIFFRACTIONr_scbond_it3.01832093
X-RAY DIFFRACTIONr_scangle_it4.414.51823
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.53→1.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 312 -
Rwork0.256 6263 -
obs--78.09 %

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