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- PDB-4d9e: D-Cysteine desulfhydrase from Salmonella typhimurium complexed wi... -

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Basic information

Entry
Database: PDB / ID: 4d9e
TitleD-Cysteine desulfhydrase from Salmonella typhimurium complexed with L-cycloserine (LCS)
ComponentsD-Cysteine desulfhydrase
KeywordsLYASE / Fold type II PLP-dependent enzyme / tryptophan synthase beta subunit like family / PLP dependent enzyme
Function / homology
Function and homology information


D-cysteine desulfhydrase / D-amino acid metabolic process / D-cysteine desulfhydrase activity
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 / Chem-LCS / D-cysteine desulfhydrase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.47 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 1.1Nov 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_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)147,88811
Polymers146,2034
Non-polymers1,6857
Water4,468248
1
A: D-Cysteine desulfhydrase
B: D-Cysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,0046
Polymers73,1012
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-16 kcal/mol
Surface area22860 Å2
MethodPISA
2
C: D-Cysteine desulfhydrase
D: D-Cysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8845
Polymers73,1012
Non-polymers7833
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-20 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.420, 165.840, 68.060
Angle α, β, γ (deg.)90.00, 119.03, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1 / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETAA1 - 32815 - 342
21HISHISBB4 - 32818 - 342
31LEULEUCC6 - 32820 - 342
41METMETDD1 - 32815 - 342
12METMETAA1 - 32815 - 342
22HISHISBB4 - 32818 - 342
32LEULEUCC6 - 32820 - 342
42METMETDD1 - 32815 - 342

NCS ensembles :
ID
1
2

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Components

#1: Protein
D-Cysteine desulfhydrase


Mass: 36550.727 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


Mass: 120.152 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical
ChemComp-LCS / [5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate


Mass: 331.219 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H14N3O7P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
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, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 9, 2010 / Details: mirrors
RadiationMonochromator: Ni mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.44→59.51 Å / Num. obs: 41742 / % possible obs: 87.3 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 8.2
Reflection shellResolution: 2.44→2.57 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4058 / % possible all: 58.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D8T

4d8t


Resolution: 2.47→58.08 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.861 / SU B: 11.07 / SU ML: 0.247 / Cross valid method: THROUGHOUT / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26274 2122 5.1 %RANDOM
Rwork0.21262 ---
obs0.21518 39608 90.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.176 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.02 Å2
2---0.03 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.47→58.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9664 0 115 248 10027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0229926
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.941.9913540
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41551308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.61124.656378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.952151498
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7511543
X-RAY DIFFRACTIONr_chiral_restr0.1220.21590
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0217504
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_it0.5641.56497
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.062210355
X-RAY DIFFRACTIONr_scbond_it1.6433429
X-RAY DIFFRACTIONr_scangle_it2.7664.53180
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2282tight positional0.130.05
11B2282tight positional0.110.05
11C2282tight positional0.10.05
11D2282tight positional0.10.05
22A22tight positional0.280.05
22B22tight positional0.460.05
22C22tight positional0.40.05
22D22tight positional0.260.05
11A2282tight thermal0.150.5
11B2282tight thermal0.150.5
11C2282tight thermal0.150.5
11D2282tight thermal0.150.5
22A22tight thermal0.230.5
22B22tight thermal0.160.5
22C22tight thermal0.170.5
22D22tight thermal0.190.5
LS refinement shellResolution: 2.466→2.53 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 119 -
Rwork0.337 2365 -
obs--72.31 %

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