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- PDB-1c7n: CRYSTAL STRUCTURE OF CYSTALYSIN FROM TREPONEMA DENTICOLA CONTAINS... -

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Basic information

Entry
Database: PDB / ID: 1c7n
TitleCRYSTAL STRUCTURE OF CYSTALYSIN FROM TREPONEMA DENTICOLA CONTAINS A PYRIDOXAL 5'-PHOSPHATE COFACTOR
ComponentsCYSTALYSIN
KeywordsTRANSFERASE / Aminotransferase / Pyridoxal phosphate
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
PYRIDOXAL-5'-PHOSPHATE / cysteine-S-conjugate beta-lyase
Similarity search - Component
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 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: Non-polymer description / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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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)372,20516
Polymers370,2288
Non-polymers1,9778
Water47,3072626
1
A: CYSTALYSIN
B: CYSTALYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0514
Polymers92,5572
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-30 kcal/mol
Surface area29750 Å2
MethodPISA
2
C: CYSTALYSIN
D: CYSTALYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0514
Polymers92,5572
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-30 kcal/mol
Surface area29570 Å2
MethodPISA
3
E: CYSTALYSIN
F: CYSTALYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0514
Polymers92,5572
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-30 kcal/mol
Surface area29650 Å2
MethodPISA
4
G: CYSTALYSIN
H: CYSTALYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0514
Polymers92,5572
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-30 kcal/mol
Surface area29650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.470, 108.440, 176.090
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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2626 / 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: 2.31 Å3/Da / Density % sol: 46.67 %
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: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 8, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. all: 382434 / Num. obs: 254989 / % possible obs: 96.5 % / Redundancy: 1.5 % / Biso Wilson estimate: 16.9 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 8.6
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.255 / Num. unique all: 12280 / % possible all: 87.9
Reflection
*PLUS
Num. measured all: 382434
Reflection shell
*PLUS
% possible obs: 87.9 %

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Processing

RefinementResolution: 1.9→25 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 12710 -RANDOM
Rwork0.208 ---
all0.231 264244 --
obs0.215 254953 96.5 %-
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25656 0 120 2626 28402
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 16.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_angle_deg1.4
X-RAY DIFFRACTIONo_dihedral_angle_deg22.5
X-RAY DIFFRACTIONo_improper_angle_deg0.87

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