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- PDB-3q4d: Crystal structure of dipeptide epimerase from Cytophaga hutchinso... -

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Basic information

Entry
Database: PDB / ID: 3q4d
TitleCrystal structure of dipeptide epimerase from Cytophaga hutchinsonii complexed with Mg and dipeptide D-Ala-L-Ala
ComponentsMandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
KeywordsISOMERASE / (beta/alpha)8-barrel
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 / peptide metabolic process / magnesium ion binding
Similarity search - Function
Dipeptide epimerase / 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 ...Dipeptide epimerase / 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
ALANINE / D-ALANINE / D-Ala-D/L-Ala epimerase
Similarity search - Component
Biological speciesCytophaga hutchinsonii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsLukk, T. / 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
DepositionDec 23, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 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 1.6Sep 13, 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_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
Revision 1.7Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
B: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
C: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
D: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
E: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
F: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
G: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
H: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
I: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)365,00436
Polymers363,1829
Non-polymers1,82227
Water2,360131
1
A: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5564
Polymers40,3541
Non-polymers2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5564
Polymers40,3541
Non-polymers2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5564
Polymers40,3541
Non-polymers2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5564
Polymers40,3541
Non-polymers2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5564
Polymers40,3541
Non-polymers2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5564
Polymers40,3541
Non-polymers2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5564
Polymers40,3541
Non-polymers2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5564
Polymers40,3541
Non-polymers2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5564
Polymers40,3541
Non-polymers2023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.560, 158.090, 182.180
Angle α, β, γ (deg.)90.00, 100.04, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein
Mandelate racemase/muconate lactonizing enzyme family; possible chloromuconate cycloisomerase


Mass: 40353.527 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cytophaga hutchinsonii (bacteria) / Strain: ATCC 33406 / Gene: CHU2140, CHU_2140, tfdD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q11T61, chloromuconate cycloisomerase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical
ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H7NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.69 Å3/Da / Density % sol: 66.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4
Details: Precipitant contained 10% PEG 4000 and 0.1M Na-citrate. Protein solution contained 0.1M NaCl, 10% glycerol, and 0.02M D-Ala-L-Ala, Protein concentration was 40 mg/mL, pH 4.0, VAPOR ...Details: Precipitant contained 10% PEG 4000 and 0.1M Na-citrate. Protein solution contained 0.1M NaCl, 10% glycerol, and 0.02M D-Ala-L-Ala, Protein concentration was 40 mg/mL, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 3, 2010
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 105392 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.138 / Net I/σ(I): 11.88
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
3-3.110.7162.4107791100
3.11-3.230.5253.210132199.9
3.23-3.380.3474.6210767199.9
3.38-3.550.2366.33100141100
3.55-3.780.1598.76109341100
3.78-4.060.09812.76101351100
4.06-4.470.07115.71106481100
4.47-5.110.05318.6710546199.9
5.11-6.40.05219.0410515199.9
6.4-200.0326.9310922198.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TKK

1tkk


Resolution: 3→20 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.886 / Cross valid method: THROUGHOUT / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25388 5256 5 %RANDOM
Rwork0.22988 ---
all0.274 105134 --
obs0.23106 99878 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0.19 Å2
2--0.15 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25434 0 108 131 25673
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02225965
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0091.9735127
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.87853312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08224.7461062
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.4154599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.17815117
X-RAY DIFFRACTIONr_chiral_restr0.0690.24086
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02119161
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.7451.516506
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it7.808226586
X-RAY DIFFRACTIONr_scbond_it9.03139459
X-RAY DIFFRACTIONr_scangle_it11.7684.58541
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 382 -
Rwork0.274 7275 -
obs--99.99 %

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