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- PDB-3fce: Crystal Structure of Bacillus cereus D-alanyl Carrier Protein Lig... -

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Basic information

Entry
Database: PDB / ID: 3fce
TitleCrystal Structure of Bacillus cereus D-alanyl Carrier Protein Ligase DltA in Complex with ATP: Implications for Adenylation Mechanism
ComponentsD-alanine--poly(phosphoribitol) ligase subunit 1
KeywordsLIGASE / DLTA / AMP-FORMING DOMAIN / D-ALANINE / ADENYLATION / D-ALANINE CARRIER PROTEIN LIGASE / ATP Complex
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, N-terminal domain / ANL, C-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, N-terminal domain / ANL, C-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. / AMP-dependent synthetase/ligase / AMP-binding enzyme / GMP Synthetase; Chain A, domain 3 / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / D-alanine--D-alanyl carrier protein ligase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsOsman, K.T. / Du, L. / He, Y. / Luo, Y.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structure of Bacillus cereus D-alanyl carrier protein ligase (DltA) in complex with ATP.
Authors: Osman, K.T. / Du, L. / He, Y. / Luo, Y.
History
DepositionNov 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...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 / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: D-alanine--poly(phosphoribitol) ligase subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,1733
Polymers57,6261
Non-polymers5472
Water7,638424
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.400, 87.400, 57.400
Angle α, β, γ (deg.)90.00, 114.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 57625.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: DltA was expressed as a fusion protein with C-terminal Histag.
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 14579 / Gene: BC_1372, 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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 CALCIUM CHLORIDE, 16% PEG 3350, 21% sucrose, PH 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Oct 25, 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: 1.9→20 Å / Num. all: 44062 / Num. obs: 38547 / % possible obs: 87.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Rmerge(I) obs: 0.06 / Rsym value: 0.06
Reflection shellResolution: 1.9→2.02 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2 / Rsym value: 0.306 / % possible all: 44.7

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
CNSrefinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3DHV

3dhv


Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1748 -RANDOM
Rwork0.207 ---
all0.207 44062 --
obs0.207 38547 87.6 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3943 0 32 424 4399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0059
X-RAY DIFFRACTIONc_angle_deg1.26

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