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- PDB-3dwi: Crystal structure of Mycobacterium tuberculosis CysM, the cystein... -

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Basic information

Entry
Database: PDB / ID: 3dwi
TitleCrystal structure of Mycobacterium tuberculosis CysM, the cysteine synthase B
ComponentsCysteine synthase B
KeywordsTRANSFERASE / Cysteine synthase / 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 / cytoplasm / cytosol
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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / O-phosphoserine sulfhydrylase / O-phosphoserine sulfhydrylase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 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 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _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: Cysteine synthase B
B: Cysteine synthase B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6107
Polymers68,8282
Non-polymers7825
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-13.1 kcal/mol
Surface area21530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.361, 85.351, 98.916
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B

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
11THRTHRGLYGLYAA2 - 292 - 29
21THRTHRGLYGLYBB2 - 292 - 29
32GLYGLYGLYGLYAA32 - 6632 - 66
42GLYGLYGLYGLYBB32 - 6632 - 66
53PROPROALAALAAA70 - 12470 - 124
63PROPROALAALABB70 - 12470 - 124
74SERSERALAALAAA129 - 132129 - 132
84SERSERALAALABB129 - 132129 - 132
95GLUGLUALAALAAA138 - 141138 - 141
105GLUGLUALAALABB138 - 141138 - 141
116TRPTRPALAALAAA146 - 201146 - 201
126TRPTRPALAALABB146 - 201146 - 201
137VALVALALAALAAA203 - 208203 - 208
147VALVALALAALABB203 - 208203 - 208
158VALVALPROPROAA227 - 233227 - 233
168VALVALPROPROBB227 - 233227 - 233
179ILEILEGLYGLYAA235 - 284235 - 284
189ILEILEGLYGLYBB235 - 284235 - 284
1910ARGARGALAALAAA286 - 305286 - 305
2010ARGARGALAALABB286 - 305286 - 305
DetailsThe asymmetric unit contains one biological unit which consists of two protomers of CysM.

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Components

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


Mass: 34413.770 Da / Num. of mol.: 2 / Mutation: K204A
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)
References: UniProt: P63873, UniProt: P9WP53*PLUS, cysteine synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.22 Å3/Da / Density % sol: 44.57 %
Crystal growpH: 7.1
Details: 0.1 M HEPES pH 7.1, 0.64 M Li2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9498
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 30, 2006
RadiationMonochromator: SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9498 Å / Relative weight: 1
ReflectionResolution: 2.81→48.22 Å / Num. obs: 15513 / % possible obs: 99.6 % / Redundancy: 5.5 % / Rsym value: 0.08 / Net I/σ(I): 18.6
Reflection shellResolution: 2.81→2.95 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.247 / % possible all: 96.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DWG, CHAIN A

3dwg


Resolution: 2.81→48.22 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.867 / SU B: 13.19 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R Free: 0.411
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.256 788 5.1 %RANDOM
Rwork0.19 ---
obs0.194 15513 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.67 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20 Å2
2---0.17 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.81→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4441 0 45 160 4646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224569
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2811.9796235
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9365601
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88122.443176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.6215662
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1611541
X-RAY DIFFRACTIONr_chiral_restr0.1970.2717
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023484
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2830.23092
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3410.23216
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.2389
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2910.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0281.53031
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51224726
X-RAY DIFFRACTIONr_scbond_it2.23331679
X-RAY DIFFRACTIONr_scangle_it3.4634.51509
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1060tight positional0.110.05
893medium positional0.50.5
1060tight thermal0.20.5
893medium thermal1.012
LS refinement shellResolution: 2.81→2.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 59 -
Rwork0.223 1010 -
obs--94.43 %

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