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- PDB-3l8c: Structure of probable D-alanine--poly(phosphoribitol) ligase subu... -

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Basic information

Entry
Database: PDB / ID: 3l8c
TitleStructure of probable D-alanine--poly(phosphoribitol) ligase subunit-1 from Streptococcus pyogenes
ComponentsD-alanine--poly(phosphoribitol) ligase subunit 1
KeywordsLIGASE / structural genomics / D-alanine-poly(phosphoribitol) ligase / dltA / 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
D-alanine--D-alanyl carrier protein ligase
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.41 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
Authors: Ramagopal, U.A. / Toro, R. / Burley, S.K. / Almo, S.C.
History
DepositionDec 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 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 / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
B: D-alanine--poly(phosphoribitol) ligase subunit 1


Theoretical massNumber of molelcules
Total (without water)116,2862
Polymers116,2862
Non-polymers00
Water1,892105
1
A: D-alanine--poly(phosphoribitol) ligase subunit 1


Theoretical massNumber of molelcules
Total (without water)58,1431
Polymers58,1431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: D-alanine--poly(phosphoribitol) ligase subunit 1


Theoretical massNumber of molelcules
Total (without water)58,1431
Polymers58,1431
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.024, 153.736, 84.794
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M6 (bacteria)
Gene: dltA, M6_Spy1043 / Plasmid: BC-pSGX4(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5XBN5, EC: 6.1.1.13
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.49 Å3/Da / Density % sol: 50.7 %
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

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 30, 2009
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 45876 / % possible obs: 99.9 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.104 / Χ2: 1.085 / Net I/σ(I): 8.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.447.90.70722130.937100
2.44-2.497.80.61222750.947100
2.49-2.537.80.55322480.922100
2.53-2.597.80.49122800.937100
2.59-2.647.80.41522630.897100
2.64-2.77.90.37522570.951100
2.7-2.777.90.30322890.921100
2.77-2.857.90.26122730.915100
2.85-2.937.90.21422720.948100
2.93-3.027.90.18122790.982100
3.02-3.137.90.14722731.066100
3.13-3.267.90.12822841.157100
3.26-3.417.80.11223161.264100
3.41-3.587.80.09422481.295100
3.58-3.817.70.08223121.245100
3.81-4.17.60.06823091.11100
4.1-4.527.40.06123191.19100
4.52-5.177.40.05923451.25499.9
5.17-6.517.60.06623681.477100
6.51-506.70.05324531.32198.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
CBASSdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.41→42.76 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.27 / WRfactor Rwork: 0.211 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.793 / SU B: 9.098 / SU ML: 0.215 / SU R Cruickshank DPI: 0.437 / SU Rfree: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.437 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS, U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.275 2319 5.1 %RANDOM
Rwork0.217 ---
all0.22 ---
obs0.22 45821 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 79.73 Å2 / Biso mean: 37.89 Å2 / Biso min: 13.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20 Å2
2---1.16 Å20 Å2
3---0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.41→42.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7841 0 0 105 7946
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228020
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.97610902
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.45951004
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.41924.837337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.788151339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7081529
X-RAY DIFFRACTIONr_chiral_restr0.1030.21244
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216035
X-RAY DIFFRACTIONr_mcbond_it0.841.55048
X-RAY DIFFRACTIONr_mcangle_it1.60128173
X-RAY DIFFRACTIONr_scbond_it2.21632972
X-RAY DIFFRACTIONr_scangle_it3.7674.52729
LS refinement shellResolution: 2.405→2.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 182 -
Rwork0.259 3045 -
all-3227 -
obs--97.76 %

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