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- PDB-4d8u: Crystal structure of D-Cysteine desulfhydrase from Salmonella typ... -

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Basic information

Entry
Database: PDB / ID: 4d8u
TitleCrystal structure of D-Cysteine desulfhydrase from Salmonella typhimurium at 3.3 A in monoclinic space group with 8 subunits in the asymmetric unit
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
PHOSPHATE ION / D-cysteine desulfhydrase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 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: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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
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

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
E: D-cysteine desulfhydrase
F: D-cysteine desulfhydrase
G: D-cysteine desulfhydrase
H: D-cysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)294,99116
Polymers294,2318
Non-polymers7608
Water32418
1
A: D-cysteine desulfhydrase
B: D-cysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7484
Polymers73,5582
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-39 kcal/mol
Surface area23360 Å2
MethodPISA
2
C: D-cysteine desulfhydrase
D: D-cysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7484
Polymers73,5582
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3470 Å2
ΔGint-40 kcal/mol
Surface area23300 Å2
MethodPISA
3
E: D-cysteine desulfhydrase
F: D-cysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7484
Polymers73,5582
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-40 kcal/mol
Surface area23530 Å2
MethodPISA
4
G: D-cysteine desulfhydrase
H: D-cysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7484
Polymers73,5582
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-40 kcal/mol
Surface area23500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)181.463, 158.140, 181.925
Angle α, β, γ (deg.)90.00, 94.10, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

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

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ALAALAAA-1 - 32813 - 342
2LEULEUBB6 - 32820 - 342
3LEULEUCC6 - 32820 - 342
4SERSERDD0 - 32814 - 342
5ALAALAEE-1 - 32813 - 342
6HISHISFF5 - 32819 - 342
7HISHISGG5 - 32819 - 342
8METMETHH-2 - 32812 - 342

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Components

#1: Protein
D-cysteine desulfhydrase /


Mass: 36778.844 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: dcyD / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) Rosetta / References: UniProt: Q8ZNT7, D-cysteine desulfhydrase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 4.42 Å3/Da / Density % sol: 72.2 %
Crystal growTemperature: 298 K / Method: microbatch method under oil / pH: 8.2
Details: 1.8M Na/K Phosphate pH 8.2, Microbatch method under oil, 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: Feb 20, 2007 / 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: 3.3→90.66 Å / Num. obs: 69703 / % possible obs: 90.7 % / Redundancy: 2.4 % / Biso Wilson estimate: 60.032 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 6.7
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 2 / Num. unique all: 9823 / % possible all: 87.9

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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: 3.3→52.04 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.859 / SU B: 27.124 / SU ML: 0.42 / Cross valid method: THROUGHOUT / ESU R Free: 0.513 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27462 3499 5 %RANDOM
Rwork0.24612 ---
obs0.24756 66132 90.38 %-
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: 66.376 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0.03 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 3.3→52.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19098 0 40 18 19156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02219507
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.691.98626673
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.15452599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80924.803735
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.979152860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6121578
X-RAY DIFFRACTIONr_chiral_restr0.1120.23153
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114762
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_it0.4481.512922
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.868220528
X-RAY DIFFRACTIONr_scbond_it1.11436585
X-RAY DIFFRACTIONr_scangle_it1.9474.56145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2152 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Atight positional0.070.05
Btight positional0.060.05
Ctight positional0.050.05
Dtight positional0.060.05
Etight positional0.050.05
Ftight positional0.060.05
Gtight positional0.060.05
Htight positional0.050.05
Atight thermal0.090.5
Btight thermal0.080.5
Ctight thermal0.070.5
Dtight thermal0.080.5
Etight thermal0.080.5
Ftight thermal0.10.5
Gtight thermal0.090.5
Htight thermal0.080.5
LS refinement shellResolution: 3.3→3.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.395 256 -
Rwork0.379 4666 -
obs--87.35 %

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