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- PDB-4cvk: PaMurF in complex with UDP-MurNAc-tripeptide (mDAP) -

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Basic information

Entry
Database: PDB / ID: 4cvk
TitlePaMurF in complex with UDP-MurNAc-tripeptide (mDAP)
Components
  • ALA-FGA-API
  • UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
KeywordsLIGASE / MURF / TRIPEPTIDE
Function / homology
Function and homology information


UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity / UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase / UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / cell cycle / cell division / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine 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-acetylmuramoyl-tripeptide--D-alanyl-D-alanine 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
N-acetyl-alpha-muramic acid / URIDINE-5'-DIPHOSPHATE / UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsRuane, K.M. / Majce, V.
CitationJournal: To be Published
Title: Pamurf in Complex with Udp-Murnac-Tripeptide (Mdap)
Authors: Majce, V. / Ruane, K.
History
DepositionMar 28, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2015Group: Structure summary
Revision 1.2Sep 23, 2015Group: Data collection
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.0Dec 7, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_asym / struct_conn / struct_ref / struct_ref_seq
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_struct_assembly.details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id
Revision 3.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_label_atom_id
Revision 3.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
B: ALA-FGA-API
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4544
Polymers49,7562
Non-polymers6972
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint6 kcal/mol
Surface area17770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.810, 87.290, 92.610
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


Mass: 49365.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: murF / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9HVZ7
#2: Protein/peptide ALA-FGA-API


Mass: 390.389 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate


Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H14N2O12P2 / Comment: UDP*YM
#4: Sugar ChemComp-MUB / N-acetyl-alpha-muramic acid / N-acetyl-muramic acid / N-ACETYLMURAMIC ACID / N-Acetylmuramic acid


Type: D-saccharide, alpha linking / Mass: 293.270 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H19NO8
IdentifierTypeProgram
a-D-GlcpNAc3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
MurNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCONTAINS A C-TERM HIS TAG

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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: 2.5 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growDetails: 0.2 M MG FORMATE, 20 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.92→49.04 Å / Num. obs: 36216 / % possible obs: 99.3 % / Observed criterion σ(I): 2.4 / Redundancy: 4.7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.2
Reflection shellResolution: 1.92→1.97 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 2.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GG4

1gg4


Resolution: 1.92→49.04 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.766 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22562 1804 5 %RANDOM
Rwork0.19568 ---
obs0.19717 34360 99.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.304 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2--1.47 Å20 Å2
3----0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.92→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3136 0 70 84 3290
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0193255
X-RAY DIFFRACTIONr_bond_other_d0.0020.023192
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9994431
X-RAY DIFFRACTIONr_angle_other_deg0.8643.0077293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.035436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.34623.846117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9215491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6691523
X-RAY DIFFRACTIONr_chiral_restr0.0930.2542
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213731
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02688
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_it1.532.2491756
X-RAY DIFFRACTIONr_mcbond_other1.5292.2491756
X-RAY DIFFRACTIONr_mcangle_it2.2623.3572188
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1642.4681499
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
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 159 -
Rwork0.26 2485 -
obs--99.62 %

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