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- PDB-4d97: Salmonella typhimurium D-Cysteine desulfhydrase with D-ser bound ... -

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Basic information

Entry
Database: PDB / ID: 4d97
TitleSalmonella typhimurium D-Cysteine desulfhydrase with D-ser bound at active site
ComponentsD-cysteine desulfhydrase
KeywordsLYASE / Fold type II PLP-dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzymes superfamily
Function / homology
Function and homology information


D-cysteine desulfhydrase / D-cysteine desulfhydrase activity / D-amino acid metabolic process
Similarity search - Function
D-cysteine desulphhydrase, bacterial / D-cysteine desulfhydrase / 1-aminocyclopropane-1-carboxylate deaminase/D-cysteine desulfhydrase / 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
BENZAMIDINE / D-SERINE / D-cysteine desulfhydrase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsBharath, S.R. / Shveta, B. / Rajesh, K.H. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: Plos One / Year: 2012
Title: Structural and Mutational Studies on Substrate Specificity and Catalysis of Salmonella typhimurium D-Cysteine Desulfhydrase.
Authors: Bharath, S.R. / Bisht, S. / Harijan, R.K. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionJan 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2012Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Structure summary
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.3Dec 6, 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

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Assembly

Deposited unit
A: D-cysteine desulfhydrase
B: D-cysteine desulfhydrase
C: D-cysteine desulfhydrase
D: D-cysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)149,85811
Polymers149,0774
Non-polymers7817
Water12,430690
1
A: D-cysteine desulfhydrase
B: D-cysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8695
Polymers74,5392
Non-polymers3303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-15 kcal/mol
Surface area22800 Å2
MethodPISA
2
C: D-cysteine desulfhydrase
D: D-cysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9896
Polymers74,5392
Non-polymers4504
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint-19 kcal/mol
Surface area23020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.445, 165.289, 68.706
Angle α, β, γ (deg.)90.00, 118.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
D-cysteine desulfhydrase /


Mass: 37269.348 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: dcyD, STM1953 / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta / References: UniProt: Q8ZNT7, D-cysteine desulfhydrase
#2: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical
ChemComp-DSN / D-SERINE / Serine


Type: D-peptide linking / Mass: 105.093 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H7NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 690 / 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: 44.59 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 1.5M Ammonium sulphate, 15% (v/v) ethylene glycol, 0.1M HEPES, 0.2% Benzamidine, 10mM D-ser, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 19, 2010 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.77→50 Å / Num. obs: 124064 / % possible obs: 99.2 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 28.14
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 1.83 / Num. unique all: 5888 / % possible all: 94.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4D8T

4d8t


Resolution: 1.77→29.13 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.937 / SU B: 3.297 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24771 6203 5 %RANDOM
Rwork0.21563 ---
obs0.21723 117261 98.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.709 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.77→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9717 0 55 690 10462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0210042
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.99413705
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.33451319
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.80324.665388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.787151544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3781545
X-RAY DIFFRACTIONr_chiral_restr0.0760.21615
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217572
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.773→1.819 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 398 -
Rwork0.32 8104 -
obs--92.83 %

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