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- PDB-1g63: PEPTIDYL-CYSTEINE DECARBOXYLASE EPID -

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Basic information

Entry
Database: PDB / ID: 1g63
TitlePEPTIDYL-CYSTEINE DECARBOXYLASE EPID
ComponentsEPIDERMIN MODIFYING ENZYME EPID
KeywordsOXIDOREDUCTASE / alpha / beta protein / Rossmann like fold
Function / homology
Function and homology information


phosphopantothenoylcysteine decarboxylase complex / phosphopantothenoylcysteine decarboxylase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases / coenzyme A biosynthetic process / FMN binding
Similarity search - Function
Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Epidermin decarboxylase
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsBlaesse, M. / Kupke, T. / Huber, R. / Steinbac, S.
Citation
Journal: EMBO J. / Year: 2000
Title: Crystal structure of the peptidyl-cysteine decarboxylase EpiD complexed with a pentapeptide substrate.
Authors: Blaesse, M. / Kupke, T. / Huber, R. / Steinbacher, S.
#1: Journal: J.Biol.Chem. / Year: 2000
Title: Molecular characterization of lantibiotic-synthesizing enzyme EpiD reveals a function for bacterial Dfp proteins in coenzyme A biosynthesis
Authors: Kupke, T. / Uebele, M. / Schmid, D. / Jung, G. / Blaesse, M. / Steinbacher, S.
History
DepositionNov 3, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: EPIDERMIN MODIFYING ENZYME EPID
B: EPIDERMIN MODIFYING ENZYME EPID
C: EPIDERMIN MODIFYING ENZYME EPID
D: EPIDERMIN MODIFYING ENZYME EPID
E: EPIDERMIN MODIFYING ENZYME EPID
F: EPIDERMIN MODIFYING ENZYME EPID
G: EPIDERMIN MODIFYING ENZYME EPID
H: EPIDERMIN MODIFYING ENZYME EPID
I: EPIDERMIN MODIFYING ENZYME EPID
J: EPIDERMIN MODIFYING ENZYME EPID
K: EPIDERMIN MODIFYING ENZYME EPID
L: EPIDERMIN MODIFYING ENZYME EPID
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,61724
Polymers250,14012
Non-polymers5,47612
Water7,494416
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39140 Å2
ΔGint-305 kcal/mol
Surface area69870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.680, 110.030, 152.870
Angle α, β, γ (deg.)90.00, 90.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
EPIDERMIN MODIFYING ENZYME EPID


Mass: 20845.031 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus epidermidis (bacteria) / Strain: TUE3298 / Gene: EPID / Plasmid: PQE12 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P30197
#2: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 416 / 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: 2.89 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.4
Details: 100 mM MES/NaOH 30% MPD , pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 %MPD1reservoir
210 mM1reservoirMgCl2
30.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.09 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 25, 1998 / Details: Double focussing X-ray optics
RadiationMonochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.09 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 213488 / Num. obs: 213488 / % possible obs: 87.1 % / Redundancy: 2.6 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 5.8 / Net I/σ(I): 10.2
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 2.8 / Rsym value: 24.8 / % possible all: 73.3
Reflection
*PLUS
Num. obs: 81936 / Num. measured all: 213488
Reflection shell
*PLUS
% possible obs: 73.3 %

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Processing

Software
NameVersionClassification
CCP4model building
CNS1refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→14.99 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2538485.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: maximum likelihood procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.263 4087 5 %RANDOM
Rwork0.23 ---
obs0.23 81936 87.1 %-
all-81936 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.65 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso mean: 39.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.35 Å20 Å2-3.71 Å2
2--5.84 Å20 Å2
3----11.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-25 Å
Luzzati sigma a0.39 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.5→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15972 0 372 416 16760
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it1.732
X-RAY DIFFRACTIONc_scangle_it2.62.5
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.369 343 5 %
Rwork0.294 6560 -
obs--73.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FMN_XPLOR_PARAMFMN_XPLOR_TOP.TXT
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.23 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 39.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.369 / % reflection Rfree: 5 % / Rfactor Rwork: 0.294

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