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- PDB-1c7o: CRYSTAL STRUCTURE OF CYSTALYSIN FROM TREPONEMA DENTICOLA CONTAINS... -

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Basic information

Entry
Database: PDB / ID: 1c7o
TitleCRYSTAL STRUCTURE OF CYSTALYSIN FROM TREPONEMA DENTICOLA CONTAINS A PYRIDOXAL 5'-PHOSPHATE-L-AMINOETHOXYVINYLGLYCINE COMPLEX
ComponentsCYSTALYSIN
KeywordsTRANSFERASE / Aminotransferase
Function / homology
Function and homology information


cysteine-S-conjugate beta-lyase / biosynthetic process / pyridoxal phosphate binding / lyase activity
Similarity search - Function
: / Putative C-S lyase / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain ...: / Putative C-S lyase / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PPG / cysteine-S-conjugate beta-lyase
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsKrupka, H.I. / Huber, R. / Holt, S.C. / Clausen, T.
CitationJournal: EMBO J. / Year: 2000
Title: Crystal structure of cystalysin from Treponema denticola: a pyridoxal 5'-phosphate-dependent protein acting as a haemolytic enzyme.
Authors: Krupka, H.I. / Huber, R. / Holt, S.C. / Clausen, T.
History
DepositionMar 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 28, 2011Group: Non-polymer description
Revision 1.4Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: CYSTALYSIN
B: CYSTALYSIN
C: CYSTALYSIN
D: CYSTALYSIN
E: CYSTALYSIN
F: CYSTALYSIN
G: CYSTALYSIN
H: CYSTALYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,34216
Polymers370,2288
Non-polymers3,1148
Water22,9511274
1
A: CYSTALYSIN
B: CYSTALYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3354
Polymers92,5572
Non-polymers7792
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-40 kcal/mol
Surface area28730 Å2
MethodPISA
2
C: CYSTALYSIN
D: CYSTALYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3354
Polymers92,5572
Non-polymers7792
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5840 Å2
ΔGint-43 kcal/mol
Surface area28720 Å2
MethodPISA
3
E: CYSTALYSIN
F: CYSTALYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3354
Polymers92,5572
Non-polymers7792
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5800 Å2
ΔGint-42 kcal/mol
Surface area28790 Å2
MethodPISA
4
G: CYSTALYSIN
H: CYSTALYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,3354
Polymers92,5572
Non-polymers7792
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-44 kcal/mol
Surface area28820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.373, 107.929, 176.156
Angle α, β, γ (deg.)90.00, 90.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
CYSTALYSIN


Mass: 46278.441 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (bacteria) / Plasmid: PLC67 / Production host: Escherichia coli (E. coli) / References: UniProt: Q56257
#2: Chemical
ChemComp-PPG / (2E,3E)-4-(2-aminoethoxy)-2-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)imino]but-3-enoic acid


Mass: 389.298 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C14H20N3O8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1274 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 4000, magnesium acetate, MES, pH 6.5, VAPOR DIFFUSION/SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
215 %(w/v)PEG40001reservoir
30.2 Mmagnesium acetate1reservoir
4100 mMMES-NaOH1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: OTHER / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 149605 / Num. obs: 106874 / % possible obs: 92.4 % / Redundancy: 1.5 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 28.9
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.204 / Num. unique all: 9997 / % possible all: 87
Reflection
*PLUS
Num. measured all: 149605
Reflection shell
*PLUS
% possible obs: 87 %

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Processing

SoftwareName: CNS / Version: 0.9 / Classification: refinement
RefinementResolution: 2.5→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.26 5379 -
Rwork0.193 --
all0.214 115851 -
obs0.201 106861 92.4 %
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25656 0 208 1274 27138
Software
*PLUS
Version: 0.9 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.4 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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