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- PDB-1iov: COMPLEX OF D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHONATE -

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Basic information

Entry
Database: PDB / ID: 1iov
TitleCOMPLEX OF D-ALA:D-ALA LIGASE WITH ADP AND A PHOSPHORYL PHOSPHONATE
ComponentsD-ALA\:D-ALA LIGASE
KeywordsLIGASE / GLYCOGEN PHOSPHORYLASE / CELL WALL / PEPTIDOGLYCAN SYNTHESIS / VANCOMYCIN / ADP BINDING
Function / homology
Function and homology information


D-alanine-D-alanine ligase / D-alanine-D-alanine ligase activity / peptidoglycan biosynthetic process / cell wall organization / regulation of cell shape / protein homodimerization activity / ATP binding / metal ion binding / 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-POB / D-alanine--D-alanine ligase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKnox, J.R. / Moews, P.C. / Fan, C.
Citation
Journal: Biochemistry / Year: 1997
Title: D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant.
Authors: Fan, C. / Park, I.S. / Walsh, C.T. / Knox, J.R.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1995
Title: A Common Fold for Peptide Synthetases Cleaving ATP to Adp
Authors: Fan, C. / Moews, P.C. / Shi, Y. / Walsh, C.T. / Knox, J.R.
#2: Journal: Science / Year: 1994
Title: Vancomycin Resistance: Structure of D-Alanine:D-Alanine Ligase at 2.3 A Resolution
Authors: Fan, C. / Moews, P.C. / Walsh, C.T. / Knox, J.R.
History
DepositionSep 20, 1996Processing site: BNL
Revision 1.0Feb 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-ALA\:D-ALA LIGASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6596
Polymers32,8681
Non-polymers7915
Water4,738263
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.600, 51.000, 51.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein D-ALA\:D-ALA LIGASE


Mass: 32867.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Description: ENZYME PROVIDED BY C.T. WALSH, HARVARD MED SCHOOL. SEE ZAWADZKE ET AL. BIOCHEM. 30, P. 1673, 1991.
Gene (production host): DDLB / Production host: Escherichia coli (E. coli) / References: UniProt: P07862, D-alanine-D-alanine ligase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#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: Chemical ChemComp-POB / 2-[(1-AMINO-ETHYL)-PHOSPHATE-PHOSPHINOYLOXY]-BUTYRIC ACID


Mass: 291.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15NO8P2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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 Å3/Da / Density % sol: 37.17 %
Crystal growpH: 6.5 / Details: AMMONIUM SULFATE, pH 6.5
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mMATP11
25 mMD-Ala-D-alpha-hydroxybutyrate phosphonate11
360 %(v/v)satammonium sulfate11
425 mMMES11
52 mM11MgCl2
62 mM11NaN3

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: 1995
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.2 Å / Num. obs: 11579 / % possible obs: 75 % / Observed criterion σ(I): 0 / Rsym value: 0.067 / Net I/σ(I): 8.8
Reflection shellResolution: 2.1→2.4 Å / % possible all: 39
Reflection
*PLUS
Num. obs: 10991 / Num. measured all: 34347 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.45 Å / % possible obs: 55 % / Num. unique obs: 3959 / Num. measured obs: 8020 / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.6

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Processing

Software
NameClassification
PROLSQrefinement
XENGENdata reduction
XENGENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DLN

2dln


Resolution: 2.2→15 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.204 -10 %
Rwork0.156 --
obs-7591 75 %
Displacement parametersBiso mean: 10.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2293 27 17 263 2600
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.02
X-RAY DIFFRACTIONp_angle_d1.1
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0190.04
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.2631
X-RAY DIFFRACTIONp_mcangle_it0.4721.5
X-RAY DIFFRACTIONp_scbond_it0.1971
X-RAY DIFFRACTIONp_scangle_it0.3561.5
X-RAY DIFFRACTIONp_plane_restr0.0050.018
X-RAY DIFFRACTIONp_chiral_restr0.1150.15
X-RAY DIFFRACTIONp_singtor_nbd0.2040.5
X-RAY DIFFRACTIONp_multtor_nbd0.3050.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.3650.5
X-RAY DIFFRACTIONp_planar_tor1.13
X-RAY DIFFRACTIONp_staggered_tor22.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor19.620
X-RAY DIFFRACTIONp_special_tor

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