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- PDB-3rit: Crystal structure of Dipeptide Epimerase from Methylococcus capsu... -

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Basic information

Entry
Database: PDB / ID: 3rit
TitleCrystal structure of Dipeptide Epimerase from Methylococcus capsulatus complexed with Mg and dipeptide L-Arg-D-Lys
ComponentsDipeptide epimerase
KeywordsISOMERASE / TIM barrel / chloromuconate cycloisomerase
Function / homology
Function and homology information


catechol-containing compound catabolic process / chloromuconate cycloisomerase activity / 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
ARGININE / D-LYSINE / L-Lys-D/L-Arg epimerase
Similarity search - Component
Biological speciesMethylococcus capsulatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.701 Å
AuthorsLukk, T. / Sakai, A. / Song, L. / Gerlt, J.A. / Nair, S.K.
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
DepositionApr 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Database references
Revision 1.3Mar 14, 2012Group: Database references
Revision 1.4Mar 21, 2012Group: Database references
Revision 1.5Mar 28, 2012Group: Database references
Revision 1.6Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)200,54449
Polymers195,4615
Non-polymers5,08344
Water9,998555
1
A: Dipeptide epimerase
C: Dipeptide epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,31320
Polymers78,1842
Non-polymers2,12918
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-38 kcal/mol
Surface area25740 Å2
MethodPISA
2
B: Dipeptide epimerase
hetero molecules

B: Dipeptide epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,64416
Polymers78,1842
Non-polymers1,46014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation15_455-x-1/2,y,-z1
Buried area2880 Å2
ΔGint-39 kcal/mol
Surface area25940 Å2
MethodPISA
3
D: Dipeptide epimerase
E: Dipeptide epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,40921
Polymers78,1842
Non-polymers2,22519
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-40 kcal/mol
Surface area26110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)275.320, 275.320, 275.320
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
11C-360-

SO4

21C-364-

1PE

31D-360-

SO4

41D-360-

SO4

51D-361-

SO4

61D-361-

SO4

71E-358-

SO4

81E-358-

SO4

91E-361-

SO4

101E-361-

SO4

DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Dipeptide epimerase / Putative chloromuconate cycloisomerase


Mass: 39092.113 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylococcus capsulatus (bacteria) / Strain: Bath / Gene: MCA1834 / Plasmid: pET-17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q607C7

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Non-polymers , 6 types, 599 molecules

#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ARG / ARGININE


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Chemical
ChemComp-DLY / D-LYSINE


Type: D-peptide linking / Mass: 146.188 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14N2O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 555 / 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: 4.45 Å3/Da / Density % sol: 72.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Precipitant contained 25% PEG 3350, 0.1M Tris-HCl, and 0.2M Li2SO4. Protein solution contained 0.1M KCl, 0.05M HEPES (pH 8.0), 0.02M L-Arg-L-Lys, and 0.01M MgCl2. Protein concentration was ...Details: Precipitant contained 25% PEG 3350, 0.1M Tris-HCl, and 0.2M Li2SO4. Protein solution contained 0.1M KCl, 0.05M HEPES (pH 8.0), 0.02M L-Arg-L-Lys, and 0.01M MgCl2. Protein concentration was 12 mg/mL, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 18, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.7→19.87 Å / Num. all: 94589 / Num. obs: 94319 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 21.5 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 12.84
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
2.7-2.80.7752.0396961100
2.8-2.910.5532.8192161100
2.91-3.040.3913.9391901100
3.04-3.20.2755.5994061100
3.2-3.40.2067.3894481100
3.4-3.660.1211.693341100
3.66-4.030.07816.4895311100
4.03-4.50.05421.180441100
4.5-5.770.04224.71107761100
5.77-19.870.03131.579948197.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_721)refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.701→19.87 Å / SU ML: 0.77 / σ(F): 1.99 / Phase error: 21.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2215 4706 5 %random
Rwork0.1752 ---
all0.228 94295 --
obs0.1775 94189 99.97 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 19.947 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.701→19.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13600 0 299 555 14454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00814090
X-RAY DIFFRACTIONf_angle_d1.33919071
X-RAY DIFFRACTIONf_dihedral_angle_d17.1425332
X-RAY DIFFRACTIONf_chiral_restr0.0962170
X-RAY DIFFRACTIONf_plane_restr0.0062490
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7013-2.73190.36111550.2992964X-RAY DIFFRACTION100
2.7319-2.7640.35141570.26962980X-RAY DIFFRACTION100
2.764-2.79760.32851580.26062988X-RAY DIFFRACTION100
2.7976-2.83290.29021550.25462962X-RAY DIFFRACTION100
2.8329-2.87010.2971560.25332955X-RAY DIFFRACTION100
2.8701-2.90930.32421550.25782952X-RAY DIFFRACTION100
2.9093-2.95070.32461560.24842959X-RAY DIFFRACTION100
2.9507-2.99460.30671570.24282986X-RAY DIFFRACTION100
2.9946-3.04120.27841560.232954X-RAY DIFFRACTION100
3.0412-3.09090.25931550.21442952X-RAY DIFFRACTION100
3.0909-3.1440.27451570.21262986X-RAY DIFFRACTION100
3.144-3.20090.25591550.21752938X-RAY DIFFRACTION100
3.2009-3.26230.27861580.21953000X-RAY DIFFRACTION100
3.2623-3.32850.2831570.20442984X-RAY DIFFRACTION100
3.3285-3.40060.26141550.19782948X-RAY DIFFRACTION100
3.4006-3.47930.21391570.18682989X-RAY DIFFRACTION100
3.4793-3.56580.22051570.17432971X-RAY DIFFRACTION100
3.5658-3.66160.21071570.17752989X-RAY DIFFRACTION100
3.6616-3.76870.22881550.17082952X-RAY DIFFRACTION100
3.7687-3.88940.22721570.16762981X-RAY DIFFRACTION100
3.8894-4.02730.17291580.14473005X-RAY DIFFRACTION100
4.0273-4.18710.18871580.14242983X-RAY DIFFRACTION100
4.1871-4.37580.18871560.14222974X-RAY DIFFRACTION1.01
4.3758-4.60380.18111570.12862979X-RAY DIFFRACTION100
4.6038-4.88820.16481580.12793002X-RAY DIFFRACTION100
4.8882-5.25910.18931580.14053011X-RAY DIFFRACTION100
5.2591-5.77650.2031590.15343007X-RAY DIFFRACTION100
5.7765-6.58560.21481580.17153005X-RAY DIFFRACTION100
6.5856-8.19910.15931600.13473047X-RAY DIFFRACTION100
8.1991-19.870.14231590.12113080X-RAY DIFFRACTION99

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