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- PDB-4bub: CRYSTAL STRUCTURE OF MURE LIGASE FROM THERMOTOGA MARITIMA IN COMP... -

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Basic information

Entry
Database: PDB / ID: 4bub
TitleCRYSTAL STRUCTURE OF MURE LIGASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH ADP
ComponentsUDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--LD-LYSINE LIGASE
KeywordsLIGASE / PEPTIDOGLYCAN SYNTHESIS / MURE / ADP-FORMING ENZYME / CELL WALL / CELL SHAPE / CELL CYCLE / NUCLEOTIDE-BINDING / ATP- BINDING / CELL DIVISION
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-D-lysine ligase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--D-lysine ligase activity / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase activity / tetrahydrofolylpolyglutamate synthase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / magnesium ion binding ...UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-D-lysine ligase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--D-lysine ligase activity / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase activity / tetrahydrofolylpolyglutamate synthase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
Folylpolyglutamate synthetase, conserved site / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / MurE/MurF, N-terminal / MurE/MurF, N-terminal domain / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal ...Folylpolyglutamate synthetase, conserved site / UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase / MurE/MurF, N-terminal / MurE/MurF, N-terminal domain / Mur ligase, N-terminal catalytic domain / Mur ligase family, catalytic domain / Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 / Mur ligase, C-terminal domain / Mur-like, catalytic domain / Mur ligase, C-terminal / Mur ligase, C-terminal domain superfamily / Mur ligase, glutamate ligase domain / 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
ADENOSINE-5'-DIPHOSPHATE / UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--LD-lysine ligase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsFavini-Stabile, S. / Contreras-Martel, C. / Thielens, N. / Dessen, A.
CitationJournal: Environ.Microbiol. / Year: 2013
Title: Mreb and Murg as Scaffolds for the Cytoplasmic Steps of Peptidoglycan Biosynthesis
Authors: Favini-Stabile, S. / Contreras-Martel, C. / Thielens, N. / Dessen, A.
History
DepositionJun 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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_database_status.status_code_sf / _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.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: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--LD-LYSINE LIGASE
B: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--LD-LYSINE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,5226
Polymers112,6192
Non-polymers9034
Water30617
1
A: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--LD-LYSINE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7613
Polymers56,3101
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--LD-LYSINE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7613
Polymers56,3101
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.387, 74.387, 441.759
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 99
2114B1 - 99
1124A100 - 325
2124B100 - 325
1134A326 - 486
2134B326 - 486

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.966187, 0.036444, -0.255254), (-0.086974, 0.885876, 0.455696), (0.242731, 0.462488, -0.852752)92.24935, -2.69733, 24.42719
3given(1), (1), (1)
4given(-0.970305, 0.032599, -0.239677), (-0.081176, 0.889524, 0.449619), (0.227856, 0.455724, -0.860464)91.80976, -2.61092, 24.90182
5given(1), (1), (1)
6given(-0.993907, -0.109651, -0.011201), (-0.108465, 0.954934, 0.276291), (-0.019599, 0.275823, -0.961009)83.61928, 3.57336, 36.46927

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Components

#1: Protein UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE--LD-LYSINE LIGASE / MURD LIGASE / D-GLUTAMIC ACID-ADDING ENZYME / UDP-N-ACETYLMURAMOYL-L-ALANYL-D-GLUTAMATE SYNTHETASE


Mass: 56309.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Strain: DSM 3109 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9WY79, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-D-lysine ligase, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate-L-lysine ligase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.24 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growpH: 5 / Details: 0.1M CITIRC ACID PH5, 3% PEGMME 5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97921
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97921 Å / Relative weight: 1
ReflectionResolution: 2.9→20 Å / Num. obs: 29228 / % possible obs: 95.9 % / Observed criterion σ(I): 3 / Redundancy: 11 % / Biso Wilson estimate: 94.853 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 40
Reflection shellResolution: 2.9→3.07 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 3 / % possible all: 81

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.9→48.48 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.919 / SU B: 25.587 / SU ML: 0.445 / Cross valid method: THROUGHOUT / ESU R Free: 0.461 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28138 2908 9.9 %RANDOM
Rwork0.21802 ---
obs0.22419 26319 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 110.399 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0.49 Å20 Å2
2---0.49 Å20 Å2
3---1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.9→48.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7547 0 56 17 7620
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0197728
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2091.98110437
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7745957
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.58923.922357
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.522151333
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4991560
X-RAY DIFFRACTIONr_chiral_restr0.0880.21190
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215750
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_it10.28610.5363840
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it15.1415.8014793
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it12.46811.353888
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A739medium positional0.690.5
12B739medium positional0.690.5
21A1758medium positional0.490.5
22B1758medium positional0.490.5
31A1258medium positional0.470.5
32B1258medium positional0.470.5
11A739medium thermal12.142
12B739medium thermal12.142
21A1758medium thermal12.042
22B1758medium thermal12.042
31A1258medium thermal9.462
32B1258medium thermal9.462
LS refinement shellResolution: 2.901→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.492 166 -
Rwork0.465 1472 -
obs--71.37 %

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