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- PDB-1tkk: The Structure of a Substrate-Liganded Complex of the L-Ala-D/L-Gl... -

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Basic information

Entry
Database: PDB / ID: 1tkk
TitleThe Structure of a Substrate-Liganded Complex of the L-Ala-D/L-Glu Epimerase from Bacillus subtilis
Componentssimilar to chloromuconate cycloisomerase
KeywordsISOMERASE / epimerase / enolase super family
Function / homology
Function and homology information


L-Ala-D/L-Glu epimerase activity / L-Ala-D/L-Glu epimerase / cell wall organization / cell wall macromolecule catabolic process / metal 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 / GLUTAMIC ACID / : / L-Ala-D/L-Glu epimerase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKlenchin, V.A. / Schmidt, D.M. / Gerlt, J.A. / Rayment, I.
CitationJournal: Biochemistry / Year: 2004
Title: Evolution of Enzymatic Activities in the Enolase Superfamily: Structure of a Substrate-Liganded Complex of the l-Ala-d/l-Glu Epimerase from Bacillus subtilis(,).
Authors: Klenchin, V.A. / Schmidt, D.M. / Gerlt, J.A. / Rayment, I.
History
DepositionJun 8, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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.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.ptnr2_label_seq_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: similar to chloromuconate cycloisomerase
B: similar to chloromuconate cycloisomerase
C: similar to chloromuconate cycloisomerase
D: similar to chloromuconate cycloisomerase
E: similar to chloromuconate cycloisomerase
F: similar to chloromuconate cycloisomerase
G: similar to chloromuconate cycloisomerase
H: similar to chloromuconate cycloisomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)318,24132
Polymers316,1578
Non-polymers2,08424
Water27,4011521
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25310 Å2
ΔGint-164 kcal/mol
Surface area86980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.4, 134.6, 194.9
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
similar to chloromuconate cycloisomerase


Mass: 39519.582 Da / Num. of mol.: 8 / Fragment: YkfB
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: Ykfb / Plasmid: pET17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 16078363, UniProt: O34508*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-ALA / ALANINE / Alanine


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H7NO2
#4: Chemical
ChemComp-GLU / GLUTAMIC ACID / Glutamic acid


Type: L-peptide linking / Mass: 147.129 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H9NO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1521 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: The protein was concentrated to 20 mg/ml and dialyzed against 5 mM HEPES, 2 mM MgCl2, 50 mM NaCl, 0.25 mM TCEP, 1 mM NaN3, pH 7.0, drop frozen as small pellets in liquid nitrogen and stored ...Details: The protein was concentrated to 20 mg/ml and dialyzed against 5 mM HEPES, 2 mM MgCl2, 50 mM NaCl, 0.25 mM TCEP, 1 mM NaN3, pH 7.0, drop frozen as small pellets in liquid nitrogen and stored at -80 C. The frozen concentrated protein was thawed and diluted to 10 mg/mL with 5 mM HEPES, 2 mM MgCl2, 1 mM NaN3, pH 7.5. A stock solution of the peptide substrate L-Ala-L-Glu (Sigma) was neutralized to pH 7.5 with NaOH and brought to a final concentration of 1.6 M. This solution was added to the protein as 1/50th part by volume and the resultant mixture utilized for crystallization experiments. The initial crystals were grown by hanging drop by mixing 5 ?l of protein solution and 5 ?l of a solution containing 9-11% dimethyl-PEG 5000, 50 mM MOPS, 1% MPD, 1 mM NaN3, pH 7.0 and suspending the droplets over 600 ?l precipitant at 20 C, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 173946 / Num. obs: 173946 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Rmerge(I) obs: 0.159 / Net I/σ(I): 8.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.6 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JPM

1jpm


Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.705 / SU ML: 0.184 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.269 / ESU R Free: 0.231 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.285 8685 5 %RANDOM
Rwork0.219 ---
all0.222 173500 --
obs0.222 164780 96.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.435 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20 Å2
2--1.87 Å20 Å2
3----0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21626 0 120 1521 23267
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02222074
X-RAY DIFFRACTIONr_bond_other_d0.0020.0220850
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.97129830
X-RAY DIFFRACTIONr_angle_other_deg0.78348536
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.73352870
X-RAY DIFFRACTIONr_chiral_restr0.0680.23502
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0224370
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024062
X-RAY DIFFRACTIONr_nbd_refined0.1920.24958
X-RAY DIFFRACTIONr_nbd_other0.220.225735
X-RAY DIFFRACTIONr_nbtor_other0.0840.213769
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.21326
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.242
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1890.2108
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1940.226
X-RAY DIFFRACTIONr_mcbond_it1.967514280
X-RAY DIFFRACTIONr_mcangle_it2.815622908
X-RAY DIFFRACTIONr_scbond_it2.63767794
X-RAY DIFFRACTIONr_scangle_it3.9337.56922
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.362 634
Rwork0.324 12064

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