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- PDB-1e8c: Structure of MurE the UDP-N-acetylmuramyl tripeptide synthetase f... -

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Basic information

Entry
Database: PDB / ID: 1e8c
TitleStructure of MurE the UDP-N-acetylmuramyl tripeptide synthetase from E. coli
ComponentsUDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
KeywordsLIGASE / PEPTIDOGLYCAN BIOSYNTHESIS
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / MurE/MurF, N-terminal domain / MurE/MurF, N-terminal / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain ...UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / MurE/MurF, N-terminal domain / MurE/MurF, N-terminal / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase family, glutamate ligase domain / Mur ligase, C-terminal domain superfamily / Mur ligase, central / Mur-like, catalytic domain superfamily / Mur ligase middle domain / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / Protein-Tyrosine Phosphatase; Chain A / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2,6-DIAMINOPIMELIC ACID / Chem-UAG / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2,6-diaminopimelate ligase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsGordon, E.J. / Chantala, L. / Dideberg, O.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: Crystal Structure of Udp-N-Acetylmuramoyl-L-Alanyl-D-Glutamate: Meso-Diaminopimelate Ligase from Escherichia Coli
Authors: Gordon, E.J. / Flouret, B. / Chantalat, L. / Van Heijenoort, J. / Mengin-Lecreulx, D. / Dideberg, O.
History
DepositionSep 19, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_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

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Assembly

Deposited unit
A: UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
B: UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9787
Polymers108,8032
Non-polymers2,1755
Water7,080393
1
A: UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5074
Polymers54,4021
Non-polymers1,1053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,4713
Polymers54,4021
Non-polymers1,0702
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.465, 99.690, 236.146
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.042, -0.999, -0.012), (0.999, 0.042, -0.011), (0.012, -0.011, 1)
Vector: 44.79782, 0.47329, 58.50714)

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Components

#1: Protein UDP-N-ACETYLMURAMOYLALANYL-D-GLUTAMATE--2,6-DIAMINOPIMELATE LIGASE


Mass: 54401.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: UDP-N-ACETYLMURAMYL-TRIPEPTIDE BOUND IN ACTIVE SITE
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Gene: MURE / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P22188, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-2,6-diaminopimelate ligase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-UAG / URIDINE-5'-DIPHOSPHATE-N-ACETYLMURAMOYL-L-ALANINE-D-GLUTAMATE


Mass: 879.608 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H43N5O23P2
#4: Chemical ChemComp-API / 2,6-DIAMINOPIMELIC ACID / Diaminopimelic acid


Type: L-peptide linking / Mass: 190.197 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14N2O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUES AFTER 494 BELONG TO LINKER AND HIS TAG USED TO EXPRESS AND PURIFY THE PROTEIN

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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: 2.8 Å3/Da / Density % sol: 47 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: HANGING DROP EXPERIMENT RESERVOIR: 13% PEG MME 5K, 0.5M LICL, 10% ISOPROPANOL, 0.1M HEPES PH 7.5, 5MM DTT, 1MM UDP-TRIPEPTIDE DROP: 2UL PROTEIN SOLUTION (MURE @ 10MGML-1 IN 20MM HEPES PH 7. ...Details: HANGING DROP EXPERIMENT RESERVOIR: 13% PEG MME 5K, 0.5M LICL, 10% ISOPROPANOL, 0.1M HEPES PH 7.5, 5MM DTT, 1MM UDP-TRIPEPTIDE DROP: 2UL PROTEIN SOLUTION (MURE @ 10MGML-1 IN 20MM HEPES PH 7.5, 200MM NACL, 5MM DTT) WITH 2UL RESERVOIR SOLUTION.
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMHEPES1drop
3200 mM1dropNaCl
45 mMdithiothreitol1drop
51 mMUMT1drop
60.1 MHEPES1reservoir
713 %PEG MME50001reservoir
80.5 M1reservoirLiCl
910 %iso-propanol1reservoir
105 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9791,0.9790,0.8550,0.93
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 15, 1999
RadiationMonochromator: GE / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.9791
30.8551
40.931
ReflectionResolution: 2→46.7 Å / Num. obs: 323548 / % possible obs: 98.3 % / Redundancy: 4.5 % / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.066
Reflection shellResolution: 2→2.13 Å / Redundancy: 3.9 % / Rsym value: 0.22 / % possible all: 91.2
Reflection
*PLUS
Num. obs: 72674 / Num. measured all: 323548 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 91.2 % / Rmerge(I) obs: 0.22

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
XDSdata reduction
SCALEPACKdata scaling
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→46.73 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3518491.82 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.23 7348 10.1 %RANDOM
Rwork0.202 ---
obs0.202 72674 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.2391 Å2 / ksol: 0.318364 e/Å3
Displacement parametersBiso mean: 34.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.81 Å20 Å20 Å2
2---0.95 Å20 Å2
3----0.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7528 0 141 393 8062
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.25 1080 10 %
Rwork0.214 9702 -
obs--87.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
LS refinement shell
*PLUS
Rfactor Rfree: 0.25

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