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- PDB-3lgx: Structure of probable D-alanine-poly(phosphoribitol) ligase subun... -

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Basic information

Entry
Database: PDB / ID: 3lgx
TitleStructure of probable D-alanine-poly(phosphoribitol) ligase subunit-1 from Streptococcus pyogenes with ATP
ComponentsD-alanine--poly(phosphoribitol) ligase subunit 1
KeywordsATP binding protein / structural genomics / ATP-binding / Cytoplasm / Nucleotide-binding / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
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 / 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 ...D-alanine--D-alanyl carrier protein ligase / 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 / 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 speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsRamagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be published
Title: Structure of probable D-alanine-poly(phosphoribitol) ligase subunit-1 from Streptococcus pyogenes with ATP
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionJan 21, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)234,6018
Polymers232,5724
Non-polymers2,0294
Water86548
1
A: D-alanine--poly(phosphoribitol) ligase subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6502
Polymers58,1431
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-alanine--poly(phosphoribitol) ligase subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6502
Polymers58,1431
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: D-alanine--poly(phosphoribitol) ligase subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6502
Polymers58,1431
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: D-alanine--poly(phosphoribitol) ligase subunit 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6502
Polymers58,1431
Non-polymers5071
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)174.410, 174.410, 176.065
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Detailsunknown

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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: 58143.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: M1 GAS / Gene: dltA, M5005_Spy1073, SPy_1312 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99ZA6, EC: 6.1.1.13
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


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


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.88 Å3/Da / Density % sol: 57.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1 M Bis-Tris pH 5.5, 25% PEG 3350, Vapor diffusion, Sitting drop, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-E10.9793
SYNCHROTRONNSLS X29A20.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDNov 5, 2009
ADSC QUANTUM 3152CCDNov 20, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 149144 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.102 / Χ2: 0.954 / Net I/σ(I): 7.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.65-2.74.20.82674630.832100
2.7-2.744.20.6974900.805100
2.74-2.84.20.67474960.891100
2.8-2.854.20.54374360.921100
2.85-2.924.20.46574580.809100
2.92-2.984.30.40175030.923100
2.98-3.064.20.39974911.341100
3.06-3.144.30.25374690.907100
3.14-3.234.30.19274600.805100
3.23-3.344.30.15674950.791100
3.34-3.464.30.13474450.861100
3.46-3.64.30.11675030.945100
3.6-3.764.20.10474551.024100
3.76-3.964.20.09875061.143100
3.96-4.214.20.08974741.105100
4.21-4.534.10.08174661.145100
4.53-4.994.10.07174961.03899.9
4.99-5.714.10.05974690.90899.8
5.71-7.194.20.05274200.92399.2
7.19-504.10.04271490.97995.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L8C

3l8c


Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.273 / WRfactor Rwork: 0.215 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.794 / SU B: 11.174 / SU ML: 0.243 / SU R Cruickshank DPI: 0.606 / SU Rfree: 0.331 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.606 / ESU R Free: 0.331 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.276 4149 5 %RANDOM
Rwork0.218 ---
obs0.221 83022 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 99.75 Å2 / Biso mean: 50.971 Å2 / Biso min: 17.49 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15888 0 124 48 16060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02216388
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.98522309
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39552031
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.91924.791695
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.835152730
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1361563
X-RAY DIFFRACTIONr_chiral_restr0.1080.22527
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02112311
X-RAY DIFFRACTIONr_mcbond_it0.8481.510187
X-RAY DIFFRACTIONr_mcangle_it1.62216519
X-RAY DIFFRACTIONr_scbond_it2.16136201
X-RAY DIFFRACTIONr_scangle_it3.6984.55790
LS refinement shellResolution: 2.604→2.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.374 282 -
Rwork0.307 5664 -
all-5946 -
obs--97.91 %

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