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- PDB-3fgp: 2.05 a Crystal Structure of CysM from Mycobacterium Tuberculosis ... -

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Basic information

Entry
Database: PDB / ID: 3fgp
Title2.05 a Crystal Structure of CysM from Mycobacterium Tuberculosis - Open and Closed Conformations
ComponentsCysteine synthase B
KeywordsTRANSFERASE / Cysteine synthase / CysM / Tuberculosis / CysO / O-phosphoserine / 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 / L-cysteine desulfhydrase activity / cysteine synthase activity / cysteine biosynthetic process / cysteine biosynthetic process from serine / pyridoxal phosphate binding / protein-containing complex / cytosol / cytoplasm
Similarity search - Function
Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
O-phosphoserine sulfhydrylase / O-phosphoserine sulfhydrylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsAgren, D. / Schnell, R. / Schneider, G.
CitationJournal: Febs Lett. / Year: 2009
Title: The C-terminal of CysM from Mycobacterium tuberculosis protects the aminoacrylate intermediate and is involved in sulfur donor selectivity
Authors: Agren, D. / Schnell, R. / Schneider, G.
History
DepositionDec 8, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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


Theoretical massNumber of molelcules
Total (without water)69,9042
Polymers69,9042
Non-polymers00
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-19 kcal/mol
Surface area24000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.933, 89.142, 99.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 34952.234 Da / Num. of mol.: 2 / Mutation: T2A
Source method: isolated from a genetically manipulated source
Details: N+terminal His+tag (Removed before crystallization)
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: cysM (Rv1336) / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P63873, UniProt: P9WP53*PLUS, O-phosphoserine sulfhydrylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.37 Å3/Da / Density % sol: 48.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1M Tris-HCl pH 7.5, 0.1M K2HPO4, 4.3M NaCl, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2008 / Details: torodial focusing mirror
RadiationMonochromator: channel cut ESRF monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.05→89.15 Å / Num. all: 41528 / Num. obs: 41528 / % possible obs: 98.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 12.2
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 2 / Num. unique all: 5922 / Rsym value: 0.554 / % possible all: 97

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DKI

3dki


Resolution: 2.05→50 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.192 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.217 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24671 2092 5 %RANDOM
Rwork0.19787 ---
obs0.20041 39379 97.66 %-
all-41528 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.818 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20 Å20 Å2
2---0.55 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4801 0 0 324 5125
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0214892
X-RAY DIFFRACTIONr_bond_other_d0.0030.023230
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9756664
X-RAY DIFFRACTIONr_angle_other_deg1.0537835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.825634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81523.077208
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.27615748
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9581544
X-RAY DIFFRACTIONr_chiral_restr0.0990.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025574
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02997
X-RAY DIFFRACTIONr_nbd_refined0.2020.21127
X-RAY DIFFRACTIONr_nbd_other0.2040.23506
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22346
X-RAY DIFFRACTIONr_nbtor_other0.0890.22632
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2311
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0930.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.218
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2580.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.29
X-RAY DIFFRACTIONr_mcbond_it0.9141.54008
X-RAY DIFFRACTIONr_mcbond_other0.1431.51311
X-RAY DIFFRACTIONr_mcangle_it1.06824983
X-RAY DIFFRACTIONr_scbond_it1.67632032
X-RAY DIFFRACTIONr_scangle_it2.3484.51681
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.05-2.1030.2981640.2382815592296.47
2.103-500.2467120920.200413937997.66

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