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- PDB-1g5q: EPID H67N COMPLEXED WITH SUBSTRATE PEPTIDE DSYTC -

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Basic information

Entry
Database: PDB / ID: 1g5q
TitleEPID H67N COMPLEXED WITH SUBSTRATE PEPTIDE DSYTC
Components
  • EPIDERMIN MODIFYING ENZYME EPID
  • LANTIBIOTIC EPIDERMIN
KeywordsOXIDOREDUCTASE / alpha / beta protein / Rossman like fold
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Carboxy-lyases / cytolysis / lyase activity / defense response to bacterium / signaling receptor binding / extracellular region
Similarity search - Function
Lantibiotic, Type A, Bacillales-type / Gallidermin / Flavin prenyltransferase-like / Flavoprotein / Flavin prenyltransferase-like / Flavoprotein / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Lantibiotic epidermin / Epidermin decarboxylase
Similarity search - Component
Biological speciesStaphylococcus epidermidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsBlaesse, M. / Kupke, T. / Huber, R. / Steinbacher, 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 2, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_special_symmetry ...database_2 / pdbx_struct_special_symmetry / 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
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: EPIDERMIN MODIFYING ENZYME EPID
M: LANTIBIOTIC EPIDERMIN
D: EPIDERMIN MODIFYING ENZYME EPID
N: LANTIBIOTIC EPIDERMIN
G: EPIDERMIN MODIFYING ENZYME EPID
O: LANTIBIOTIC EPIDERMIN
L: EPIDERMIN MODIFYING ENZYME EPID
P: LANTIBIOTIC EPIDERMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,70414
Polymers85,6348
Non-polymers2,0706
Water2,450136
1
A: EPIDERMIN MODIFYING ENZYME EPID
M: LANTIBIOTIC EPIDERMIN
D: EPIDERMIN MODIFYING ENZYME EPID
N: LANTIBIOTIC EPIDERMIN
G: EPIDERMIN MODIFYING ENZYME EPID
O: LANTIBIOTIC EPIDERMIN
L: EPIDERMIN MODIFYING ENZYME EPID
P: LANTIBIOTIC EPIDERMIN
hetero molecules

A: EPIDERMIN MODIFYING ENZYME EPID
M: LANTIBIOTIC EPIDERMIN
D: EPIDERMIN MODIFYING ENZYME EPID
N: LANTIBIOTIC EPIDERMIN
G: EPIDERMIN MODIFYING ENZYME EPID
O: LANTIBIOTIC EPIDERMIN
L: EPIDERMIN MODIFYING ENZYME EPID
P: LANTIBIOTIC EPIDERMIN
hetero molecules

A: EPIDERMIN MODIFYING ENZYME EPID
M: LANTIBIOTIC EPIDERMIN
D: EPIDERMIN MODIFYING ENZYME EPID
N: LANTIBIOTIC EPIDERMIN
G: EPIDERMIN MODIFYING ENZYME EPID
O: LANTIBIOTIC EPIDERMIN
L: EPIDERMIN MODIFYING ENZYME EPID
P: LANTIBIOTIC EPIDERMIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,11242
Polymers256,90324
Non-polymers6,20918
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_645-z+1,x-1/2,-y+1/21
crystal symmetry operation11_556y+1/2,-z+1/2,-x+11
Buried area62120 Å2
ΔGint-352 kcal/mol
Surface area66170 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)223.552, 223.552, 223.552
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-402-

TRS

21A-402-

TRS

DetailsThe biological assembly is a dodecamer generated from the tetramer in the asymmetric unit by the operations: -z+1, x-1/2, -y+1/2 and y+1/2, -z+1/2, -x+1.

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Components

#1: Protein
EPIDERMIN MODIFYING ENZYME EPID


Mass: 20820.986 Da / Num. of mol.: 4 / Mutation: H67N
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: Protein/peptide
LANTIBIOTIC EPIDERMIN


Mass: 587.601 Da / Num. of mol.: 4 / Fragment: C-TERMINUS / Mutation: N401D C404T / Source method: obtained synthetically / Details: The pentapeptide was chemically sythesized. / References: UniProt: P08136
#3: Chemical
ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE / Flavin mononucleotide


Mass: 456.344 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 5.82 Å3/Da / Density % sol: 79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM MES/NaOH, 30 % MPD, 10 mM Peptide DSYTC, 3 mM DTT, 120 mM Glycine, pH 6.5, 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: 1.0499 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2000
RadiationMonochromator: double crystal monochromator, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0499 Å / Relative weight: 1
ReflectionResolution: 2.57→20 Å / Num. all: 151692 / Num. obs: 151692 / % possible obs: 93.2 % / Redundancy: 2.7 % / Biso Wilson estimate: 47.1 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 6.8 / Net I/σ(I): 12.2
Reflection shellResolution: 2.57→2.68 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2 / Num. unique all: 5205 / % possible all: 59.4
Reflection
*PLUS
Num. obs: 56352 / Num. measured all: 151692
Reflection shell
*PLUS
% possible obs: 59.4 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: tetramer from EpiD

Resolution: 2.57→19.92 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3587123.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: used maximum likelihood procedure
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2881 5.1 %RANDOM
Rwork0.209 ---
all-56352 --
obs-56352 95.8 %-
Displacement parametersBiso mean: 50 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.33 Å
Luzzati d res low-25 Å
Luzzati sigma a0.33 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.57→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5764 0 140 136 6040
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONo_bond_d0.008
X-RAY DIFFRACTIONo_angle_deg1.3
X-RAY DIFFRACTIONo_dihedral_angle_d22.9
X-RAY DIFFRACTIONo_improper_angle_d0.9
X-RAY DIFFRACTIONo_mcbond_it1.221.5
X-RAY DIFFRACTIONo_mcangle_it2.062
X-RAY DIFFRACTIONo_scbond_it2.062
X-RAY DIFFRACTIONo_scangle_it3.122.5
Refine LS restraints NCSNCS model details: CONSTRAINED
LS refinement shellResolution: 2.57→2.66 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.328 189 4.8 %
Rwork0.311 3761 -
obs--67.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2FMN_XPLOR_PARAMFMN_XPLOR_TOP.TXT
X-RAY DIFFRACTION3TRIS_XPLOR_PARAMTRIS_XPLOR_TOP.TXT
X-RAY DIFFRACTION4WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 % / Rfactor obs: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 50 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.9
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: 0.328 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.311

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