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- PDB-1e4e: D-alanyl-D-lacate ligase -

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Basic information

Entry
Database: PDB / ID: 1e4e
TitleD-alanyl-D-lacate ligase
Components(VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN ...) x 2
KeywordsLIGASE / CELL WALL / ANTIBIOTIC RESISTANCE / MEMBRANE / PEPTIDOGLYCAN SYNTHESIS
Function / homology
Function and homology information


D-alanine-(R)-lactate ligase / D-alanine-(R)-lactate ligase activity / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / response to antibiotic / ATP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / D-alanine--D-alanine ligase, C-terminal / D-ala D-ala ligase C-terminus / Rossmann fold - #20 / ATP-grasp fold, A domain ...D-alanine--D-alanine ligase/VANA/B/C, conserved site / D-alanine--D-alanine ligase / D-alanine--D-alanine ligase, N-terminal domain / D-ala D-ala ligase N-terminus / D-alanine--D-alanine ligase signature 1. / D-alanine--D-alanine ligase signature 2. / D-alanine--D-alanine ligase, C-terminal / D-ala D-ala ligase C-terminus / Rossmann fold - #20 / ATP-grasp fold, A domain / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold, B domain / ATP-grasp fold / ATP-grasp fold profile. / D-amino Acid Aminotransferase; Chain A, domain 1 / Dna Ligase; domain 1 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Chem-PHY / Vancomycin/teicoplanin A-type resistance protein VanA
Similarity search - Component
Biological speciesENTEROCOCCUS FAECIUM (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRoper, D.I.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2000
Title: The molecular basis of vancomycin resistance in clinically relevant Enterococci: crystal structure of D-alanyl-D-lactate ligase (VanA).
Authors: Roper, D.I. / Huyton, T. / Vagin, A. / Dodson, G.
History
DepositionJul 3, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2001Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2011Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Sep 13, 2017Group: Advisory / Database references / Category: citation / pdbx_unobs_or_zero_occ_atoms
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.3Oct 9, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status ...exptl_crystal_grow / pdbx_database_status / reflns / reflns_shell
Item: _exptl_crystal_grow.method / _pdbx_database_status.status_code_sf ..._exptl_crystal_grow.method / _pdbx_database_status.status_code_sf / _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _reflns_shell.meanI_over_sigI_obs
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.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_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
Revision 1.5Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA
B: VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,27327
Polymers75,1932
Non-polymers3,07925
Water6,395355
1
A: VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA
B: VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA
hetero molecules

A: VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA
B: VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,54554
Polymers150,3864
Non-polymers6,15950
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area22480 Å2
ΔGint-282.1 kcal/mol
Surface area47970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.204, 225.359, 72.439
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: (-0.57983, -0.49666, -0.64586), (-0.47548, -0.43744, 0.76326), (-0.6616, 0.74965, 0.01748)
Vector: 96.74762, 45.15613, 28.34869)

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Components

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VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN ... , 2 types, 2 molecules AB

#1: Protein VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA / D-ALANINE--D-LACTATE LIGASE / VANA LIGASE


Mass: 37575.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROCOCCUS FAECIUM (bacteria) / Strain: BM41417 / Cellular location: CYTOPLASM / Gene: VANA / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P25051, D-alanine-(R)-lactate ligase
#2: Protein VANCOMYCIN/TEICOPLANIN A-TYPE RESISTANCE PROTEIN VANA / D-ALANINE--D-LACTATE LIGASE / VANA LIGASE


Mass: 37618.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROCOCCUS FAECIUM (bacteria) / Strain: BM41417 / Cellular location: CYTOPLASM / Gene: VANA / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P25051, D-alanine-(R)-lactate ligase

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Non-polymers , 6 types, 380 molecules

#3: 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
#4: Chemical ChemComp-PHY / 1(S)-AMINOETHYL-(2-CARBOXYPROPYL)PHOSPHORYL-PHOSPHINIC ACID


Mass: 275.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H15NO7P2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsCHAIN A AND CHAIN B DIFFER AT RESIDUE 298

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.13 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6.5 / Details: pH 6.50
Crystal grow
*PLUS
pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
140-45 %ammonium sulfate1reservoir
20.1 MMOPS1reservoirpH6.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorDate: Jan 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→15 Å / Num. obs: 32814 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 1 % / Biso Wilson estimate: 41.66 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 29.9
Reflection shellResolution: 2.5→2.54 Å / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.1 / % possible all: 96.6
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 96.6 % / Rmerge(I) obs: 0.217 / Mean I/σ(I) obs: 4.1

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Processing

Software
NameClassification
REFMACrefinement
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1IOW

1iow


Resolution: 2.5→15 Å / SU B: 0.191 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.39 / ESU R Free: 0.29
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1664 5 %RANDOM
Rwork0.183 ---
obs-32814 93.3 %-
Displacement parametersBiso mean: 44.8 Å2
Baniso -1Baniso -2Baniso -3
1-1.75 Å20 Å20 Å2
2---1.3 Å20 Å2
3----0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5210 0 185 355 5750
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0280.021
X-RAY DIFFRACTIONp_angle_d0.490.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0520.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.0332
X-RAY DIFFRACTIONp_mcangle_it3.1413
X-RAY DIFFRACTIONp_scbond_it2.6052
X-RAY DIFFRACTIONp_scangle_it3.8743
X-RAY DIFFRACTIONp_plane_restr0.0270.03
X-RAY DIFFRACTIONp_chiral_restr0.1730.15
X-RAY DIFFRACTIONp_singtor_nbd0.2040.3
X-RAY DIFFRACTIONp_multtor_nbd0.3080.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.2250.3
X-RAY DIFFRACTIONp_planar_tor4.57
X-RAY DIFFRACTIONp_staggered_tor19.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor28.620
X-RAY DIFFRACTIONp_special_tor15
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / Rfactor obs: 0.183 / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d0.039

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