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- PDB-4d9b: Pyridoxamine 5' phosphate (PMP) bound form of Salmonella typhimur... -

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Basic information

Entry
Database: PDB / ID: 4d9b
TitlePyridoxamine 5' phosphate (PMP) bound form of Salmonella typhimurium D-Cysteine desulfhydrase obtained after co-crystallization with D-cycloserine
ComponentsD-cysteine desulfhydrase
KeywordsLYASE / Fold type II PLP-dependent enzyme or 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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BENZAMIDINE / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / D-cysteine desulfhydrase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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_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_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)147,92817
Polymers146,2034
Non-polymers1,72613
Water15,979887
1
A: D-cysteine desulfhydrase
B: D-cysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9669
Polymers73,1012
Non-polymers8657
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5240 Å2
ΔGint-6 kcal/mol
Surface area22880 Å2
MethodPISA
2
C: D-cysteine desulfhydrase
D: D-cysteine desulfhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9628
Polymers73,1012
Non-polymers8616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-13 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.318, 164.926, 68.314
Angle α, β, γ (deg.)90.00, 118.97, 90.00
Int Tables number4
Space group name H-MP1211

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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-PMP / 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE / PYRIDOXAMINE-5'-PHOSPHATE


Mass: 248.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13N2O5P
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 887 / 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: 44.98 %
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-Cycloserine, 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 torroid
RadiationMonochromator: Si(III) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 143652 / % possible obs: 96.9 % / Redundancy: 4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 33.94
Reflection shellResolution: 1.67→1.73 Å / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 3.68 / % possible all: 89.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4D8T

4d8t


Resolution: 1.67→39.91 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.037 / SU ML: 0.068 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20593 7191 5 %RANDOM
Rwork0.17054 ---
obs0.17231 136354 97.5 %-
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: 22.025 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20.01 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.67→39.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9685 0 115 887 10687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.02210088
X-RAY DIFFRACTIONr_angle_refined_deg2.2311.98913763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51651328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04624.552391
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.644151567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0941547
X-RAY DIFFRACTIONr_chiral_restr0.1710.21620
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0217614
X-RAY DIFFRACTIONr_mcbond_it1.3991.56534
X-RAY DIFFRACTIONr_mcangle_it2.183210455
X-RAY DIFFRACTIONr_scbond_it3.37633554
X-RAY DIFFRACTIONr_scangle_it5.1324.53297
LS refinement shellResolution: 1.673→1.717 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 522 -
Rwork0.251 9765 -
obs--95 %

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