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- PDB-3dhv: Crystal structure of DltA protein in complex with D-alanine adenylate -

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Basic information

Entry
Database: PDB / ID: 3dhv
TitleCrystal structure of DltA protein in complex with D-alanine adenylate
ComponentsD-alanine-poly(phosphoribitol) ligaseD-alanine—poly(phosphoribitol) ligase
KeywordsLIGASE / DltA / AMP-forming domain / D-alanine / Adenylation / D-alanine carrier protein ligase / Cytoplasm
Function / homology
Function and homology information


D-alanine-[D-alanyl-carrier protein] ligase / D-alanine [D-alanyl carrier protein] ligase activity / lipoteichoic acid biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
D-alanine--D-alanyl carrier protein ligase / D-alanine:D-alanyl carrier protein ligase-like / ANL, C-terminal domain / ANL, N-terminal domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. ...D-alanine--D-alanyl carrier protein ligase / D-alanine:D-alanyl carrier protein ligase-like / ANL, C-terminal domain / ANL, N-terminal domain / Amino acid adenylation domain / ANL, N-terminal domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / GMP Synthetase; Chain A, domain 3 / AMP-dependent synthetase/ligase / AMP-binding enzyme, C-terminal domain superfamily / AMP-binding enzyme / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / D-ALANINE / D-alanine--D-alanyl carrier protein ligase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDu, L. / He, Y. / Luo, Y.
CitationJournal: Biochemistry / Year: 2008
Title: Crystal structure and enantiomer selection by D-alanyl carrier protein ligase DltA from Bacillus cereus.
Authors: Du, L. / He, Y. / Luo, Y.
History
DepositionJun 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: D-alanine-poly(phosphoribitol) ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0023
Polymers57,5661
Non-polymers4362
Water3,549197
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.700, 86.700, 57.400
Angle α, β, γ (deg.)90.00, 113.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein D-alanine-poly(phosphoribitol) ligase / D-alanine—poly(phosphoribitol) ligase / D- alanine-activating enzyme / DAE / D-alanine-D-alanyl carrier protein ligase / DCL


Mass: 57565.594 Da / Num. of mol.: 1 / Mutation: M1A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: dltA / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Rosetta2 (DE3) / References: UniProt: Q81G39, EC: 6.1.1.13
#2: Chemical ChemComp-DAL / D-ALANINE / Alanine


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.05 M Hepes, 0.2 M potassium chloride, 0.1 M Magnesium chloride, 12% PEG 3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 294.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Apr 11, 2008 / Details: mirrors
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 37000 / Num. obs: 35392 / % possible obs: 95.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 8
Reflection shellResolution: 2→2.09 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4693 / Rsym value: 0.265 / % possible all: 76.2

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
AMoREphasing
CNS1.1refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AMU

1amu


Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1748 -RANDOM
Rwork0.213 ---
all0.213 37000 --
obs0.213 35313 95.4 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3934 0 28 197 4159
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.26

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