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- PDB-3zl8: CRYSTAL STRUCTURE OF MURF LIGASE FROM THERMOTOGA MARITIMA IN COMP... -

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Basic information

Entry
Database: PDB / ID: 3zl8
TitleCRYSTAL STRUCTURE OF MURF LIGASE FROM THERMOTOGA MARITIMA IN COMPLEX WITH ADP
ComponentsUDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE
KeywordsLIGASE / PEPTIDOGLYCAN SYNTHESIS / ADP-FORMING ENZYME / CELL WALL / CELL SHAPE / CELL CYCLE / NUCLEOTIDE-BINDING / ATP-BINDING / CELL DIVISION
Function / homology
Function and homology information


UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase / UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity / UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell division / ATP binding / cytoplasm
Similarity search - Function
: / UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine 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 ...: / UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine 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-tripeptide--D-alanyl-D-alanine ligase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.65 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
DepositionJan 29, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _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-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,7713
Polymers49,2511
Non-polymers5192
Water4,774265
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.229, 49.595, 177.164
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 UDP-N-ACETYLMURAMOYL-TRIPEPTIDE--D-ALANYL-D-ALANINE LIGASE / MURF LIGASE


Mass: 49251.484 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q9WY78, UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.16 Å3/Da / Density % sol: 43.02 % / Description: NONE
Crystal growpH: 5.5
Details: 0.1M SODIUM ACETATE PH 5.5, 45-49%(V/V) 2-METHYL-2,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97932
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.65→46.54 Å / Num. obs: 50746 / % possible obs: 96 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 28.741 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 30.9
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3 / % possible all: 91.7

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Processing

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

Resolution: 1.65→46.54 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.755 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.21981 5117 10.1 %RANDOM
Rwork0.16373 ---
obs0.16935 45628 96.47 %-
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: 25.235 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å20 Å2
2---0.77 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.65→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3379 0 33 265 3677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193476
X-RAY DIFFRACTIONr_bond_other_d0.0010.023419
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.9874685
X-RAY DIFFRACTIONr_angle_other_deg0.63937878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9765428
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39423.791153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.32715648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4111526
X-RAY DIFFRACTIONr_chiral_restr0.0810.2529
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023836
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02767
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_it2.0991.1311709
X-RAY DIFFRACTIONr_mcbond_other2.0881.1311708
X-RAY DIFFRACTIONr_mcangle_it2.3961.7032135
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3781.6321767
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_restr5.2336895
X-RAY DIFFRACTIONr_sphericity_free30.357596
X-RAY DIFFRACTIONr_sphericity_bonded8.3957004
LS refinement shellResolution: 1.646→1.688 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 322 -
Rwork0.319 3026 -
obs--88.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.08411.3475-0.79514.3234-1.05562.6410.0873-0.01050.20360.0327-0.05110.3028-0.0218-0.0872-0.03620.00450.00480.00560.0515-0.0130.11572.802214.18545.7991
20.81870.41330.39490.90150.62631.829-0-0.17510.15360.1338-0.0444-0.0061-0.05430.00410.04440.04510.012-0.00730.0592-0.01880.06034.05160.1403-0.2531
31.68951.08420.23814.97870.7392.3118-0.03360.07530.1966-0.2254-0.0747-0.0003-0.1785-0.12060.10830.03370.01780.00470.1043-0.01570.0664-2.9292-2.7703-4.3936
41.1029-0.03610.36451.0225-0.23351.6098-0.02340.08580.0273-0.05150.03620.01530.037-0.0563-0.01280.0444-0.00350.00360.0712-0.00510.0482.617-12.5696-19.7958
51.77260.5280.15581.8386-0.11721.6057-0.0506-0.02020.0062-0.02440.03710.0115-0.10120.01130.01350.0977-0.0102-0.03280.08020.0110.04211.477.1406-36.0545
615.51037.556411.85225.7972-4.54714.0828-0.1512-0.62640.9954-0.5231-0.33550.8126-0.2212-0.7090.48670.5580.40830.13980.33210.12290.3451-16.505116.3194-38.698
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 50
2X-RAY DIFFRACTION2A51 - 104
3X-RAY DIFFRACTION3A105 - 137
4X-RAY DIFFRACTION4A138 - 298
5X-RAY DIFFRACTION5A299 - 422
6X-RAY DIFFRACTION6A423 - 427

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