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

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Basic information

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


racemase and epimerase activity, acting on amino acids and derivatives / racemase and epimerase activity / Isomerases; Racemases and epimerases; Acting on amino acids and derivatives / amino acid catabolic process / peptide metabolic 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
LEUCINE / 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 24, 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)305,45832
Polymers302,7658
Non-polymers2,69324
Water7,620423
1
A: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1824
Polymers37,8461
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1824
Polymers37,8461
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1824
Polymers37,8461
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1824
Polymers37,8461
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1824
Polymers37,8461
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1824
Polymers37,8461
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1824
Polymers37,8461
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1824
Polymers37,8461
Non-polymers3373
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
A: Dipeptide Epimerase
B: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3658
Polymers75,6912
Non-polymers6736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-10 kcal/mol
Surface area25060 Å2
MethodPISA
10
C: Dipeptide Epimerase
D: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3658
Polymers75,6912
Non-polymers6736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-9 kcal/mol
Surface area25120 Å2
MethodPISA
11
E: Dipeptide Epimerase
F: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3658
Polymers75,6912
Non-polymers6736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-21 kcal/mol
Surface area24970 Å2
MethodPISA
12
G: Dipeptide Epimerase
H: Dipeptide Epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,3658
Polymers75,6912
Non-polymers6736
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-19 kcal/mol
Surface area24950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.855, 163.855, 318.684
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a monomer

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Components

#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
#2: Chemical
ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13NO2
#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-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2.0M ammonium sulfate, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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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: Sep 4, 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: 205342 / Num. obs: 205342 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.078

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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→24.77 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3471640.69 / 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
Rfree0.281 10297 5 %RANDOM
Rwork0.247 ---
all0.248 205342 --
obs0.247 205342 95.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9832 Å2 / ksol: 0.365076 e/Å3
Displacement parametersBiso mean: 39.8 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å23.87 Å20 Å2
2--2.92 Å20 Å2
3----5.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2→24.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21170 0 176 423 21769
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it1.251.5
X-RAY DIFFRACTIONc_mcangle_it1.82
X-RAY DIFFRACTIONc_scbond_it2.012
X-RAY DIFFRACTIONc_scangle_it2.912.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.326 1049 4.9 %
Rwork0.29 20481 -
obs-20481 99.9 %
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 DIFFRACTION4&_1_PARAMETER_INFILE_4&_1_TOPOLOGY_INFILE_4
X-RAY DIFFRACTION5&_1_PARAMETER_INFILE_5&_1_TOPOLOGY_INFILE_5

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