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- PDB-3k1g: Crystal structure of Dipeptide Epimerase from Enterococcus faecal... -

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Basic information

Entry
Database: PDB / ID: 3k1g
TitleCrystal structure of Dipeptide Epimerase from Enterococcus faecalis V583 complexed with Mg and dipeptide L-Ser-L-Tyr
ComponentsDipeptide Epimerase
KeywordsISOMERASE / Dipeptide Epimerase / Enolase superfamily / L-Ser-L-Tyr
Function / homology
Function and homology information


racemase and epimerase activity / racemase and epimerase activity, acting on amino acids and derivatives / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / peptide metabolic process / amino acid catabolic process / magnesium ion binding
Similarity search - Function
Dipeptide epimerase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain ...Dipeptide epimerase / Mandelate racemase / muconate lactonizing enzyme family signature 2. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
SERINE / TYROSINE / Hydrophobic dipeptide epimerase
Similarity search - Component
Biological speciesEnterococcus faecalis V583 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Imker, H.J. / Sakai, A. / Gerlt, J.A. / Almo, S.C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Homology models guide discovery of diverse enzyme specificities among dipeptide epimerases in the enolase superfamily.
Authors: Lukk, T. / Sakai, A. / Kalyanaraman, C. / Brown, S.D. / Imker, H.J. / Song, L. / Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Hillerich, B. / Seidel, R. / Patskovsky, Y. / Vetting, M.W. / ...Authors: Lukk, T. / Sakai, A. / Kalyanaraman, C. / Brown, S.D. / Imker, H.J. / Song, L. / Fedorov, A.A. / Fedorov, E.V. / Toro, R. / Hillerich, B. / Seidel, R. / Patskovsky, Y. / Vetting, M.W. / Nair, S.K. / Babbitt, P.C. / Almo, S.C. / Gerlt, J.A. / Jacobson, M.P.
History
DepositionSep 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3May 23, 2012Group: Database references
Revision 1.4Sep 6, 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _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: Dipeptide Epimerase
B: Dipeptide Epimerase
C: Dipeptide Epimerase
D: Dipeptide Epimerase
E: Dipeptide Epimerase
F: Dipeptide Epimerase
G: Dipeptide Epimerase
H: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)305,98640
Polymers302,7658
Non-polymers3,22132
Water8,737485
1
A: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2485
Polymers37,8461
Non-polymers4034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2485
Polymers37,8461
Non-polymers4034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2485
Polymers37,8461
Non-polymers4034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2485
Polymers37,8461
Non-polymers4034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2485
Polymers37,8461
Non-polymers4034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2485
Polymers37,8461
Non-polymers4034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2485
Polymers37,8461
Non-polymers4034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2485
Polymers37,8461
Non-polymers4034
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: Dipeptide Epimerase
B: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,49710
Polymers75,6912
Non-polymers8058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-12 kcal/mol
Surface area24890 Å2
MethodPISA
10
C: Dipeptide Epimerase
D: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,49710
Polymers75,6912
Non-polymers8058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-11 kcal/mol
Surface area24990 Å2
MethodPISA
11
E: Dipeptide Epimerase
F: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,49710
Polymers75,6912
Non-polymers8058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-22 kcal/mol
Surface area24910 Å2
MethodPISA
12
G: Dipeptide Epimerase
H: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,49710
Polymers75,6912
Non-polymers8058
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-13 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.663, 163.663, 318.051
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Detailsauthors state that the biological assembly is a monomer

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Dipeptide Epimerase / Mandelate racemase/muconate lactonizing enzyme family protein


Mass: 37845.629 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis V583 (bacteria) / Gene: EF_1511 / Production host: Escherichia coli (E. coli) / References: UniProt: Q834W6

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Non-polymers , 5 types, 517 molecules

#2: Chemical
ChemComp-SER / SERINE


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7NO3
#3: Chemical
ChemComp-TYR / TYROSINE


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H11NO3
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.57 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M Sodium Citrate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 21, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. all: 214313 / Num. obs: 214313 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 25.7 Å2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
BALBESphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JVA

3jva


Resolution: 2→24.73 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2468139.28 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 10752 5 %RANDOM
Rwork0.245 ---
all0.247 214313 --
obs0.245 214313 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.02 Å2 / ksol: 0.364513 e/Å3
Displacement parametersBiso mean: 41.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å23.21 Å20 Å2
2--1.1 Å20 Å2
3----2.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21170 0 208 485 21863
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.231.5
X-RAY DIFFRACTIONc_mcangle_it1.852
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.832.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.373 1057 5 %
Rwork0.357 20236 -
obs-20236 99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4GOL_xplor_par.txtGOL_xplor_top.txt
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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