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- PDB-4rww: Crystal Structure of L. monocytogenes PstA in complex with cyclic... -

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Basic information

Entry
Database: PDB / ID: 4rww
TitleCrystal Structure of L. monocytogenes PstA in complex with cyclic-di-AMP
ComponentsLmo2692 protein
KeywordsPROTEIN BINDING / PII-like
Function / homology
Function and homology information


Cyclic-di-AMP receptor / Cyclic-di-AMP receptor / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-2BA / Lmo2692 protein
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChoi, P.H. / Tong, L.
CitationJournal: Microbiologyopen / Year: 2015
Title: Molecular basis for the recognition of cyclic-di-AMP by PstA, a PII -like signal transduction protein.
Authors: Choi, P.H. / Sureka, K. / Woodward, J.J. / Tong, L.
History
DepositionDec 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 1, 2015Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_sheet / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lmo2692 protein
B: Lmo2692 protein
C: Lmo2692 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6637
Polymers37,0293
Non-polymers2,6344
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7260 Å2
ΔGint-46 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.108, 51.788, 52.996
Angle α, β, γ (deg.)110.80, 105.59, 109.84
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Lmo2692 protein


Mass: 12343.028 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: ATCC BAA-679 / EGD-e / Gene: lmo2692 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y3Y7
#2: Chemical
ChemComp-2BA / (2R,3R,3aS,5R,7aR,9R,10R,10aS,12R,14aR)-2,9-bis(6-amino-9H-purin-9-yl)octahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8 ]tetraoxadiphosphacyclododecine-3,5,10,12-tetrol 5,12-dioxide / bis-(3',5')-cyclic-dimeric-Adenosine-monophosphate


Mass: 658.412 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N10O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.99 Å3/Da / Density % sol: 58.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4
Details: pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 54378 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.7
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 3.2 / % possible all: 94.6

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3M05

3m05


Resolution: 1.6→29.58 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.36 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.071 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19446 2750 5.1 %RANDOM
Rwork0.15722 ---
obs0.15909 51628 96.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.624 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å2-0.44 Å2-0.59 Å2
2---0.13 Å2-0.52 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2472 0 176 297 2945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0192770
X-RAY DIFFRACTIONr_bond_other_d0.0010.022537
X-RAY DIFFRACTIONr_angle_refined_deg1.6932.0393799
X-RAY DIFFRACTIONr_angle_other_deg0.73335856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.91525.135111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88415439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.432159
X-RAY DIFFRACTIONr_chiral_restr0.110.2440
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0213032
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02615
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.601→1.688 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.302 365 -
Rwork0.246 7313 -
obs--93.6 %

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