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- PDB-4rwx: Crystal Structure of L. monocytogenes PstA -

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Basic information

Entry
Database: PDB / ID: 4rwx
TitleCrystal Structure of L. monocytogenes PstA
ComponentsLmo2692 protein
KeywordsPROTEIN BINDING / PII-like
Function / homologyCyclic-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 / Lmo2692 protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 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 1.2Feb 28, 2024Group: 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)37,4443
Polymers37,4443
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-46 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.879, 61.634, 83.472
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHEAA1 - 1091 - 109
21PHEPHEBB1 - 1091 - 109
12PHEPHEAA1 - 1091 - 109
22PHEPHECC1 - 1091 - 109
13HISHISBB1 - 1131 - 113
23HISHISCC1 - 1131 - 113

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Lmo2692 protein


Mass: 12481.175 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

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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: 1.92 Å3/Da / Density % sol: 35.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: pH 5.5, 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: 2.9→50 Å / Num. obs: 6725 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.4
Reflection shellResolution: 2.9→3 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.9→41.77 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.917 / SU B: 19.684 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.406 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26162 326 4.7 %RANDOM
Rwork0.22436 ---
obs0.22615 6541 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 82.03 Å2
Baniso -1Baniso -2Baniso -3
1-6.74 Å2-0 Å2-0 Å2
2---2.28 Å20 Å2
3----4.46 Å2
Refinement stepCycle: LAST / Resolution: 2.9→41.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1831 0 0 0 1831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0191854
X-RAY DIFFRACTIONr_bond_other_d0.0050.021786
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9292492
X-RAY DIFFRACTIONr_angle_other_deg1.15534092
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2755228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.37925.11488
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.35115322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.108157
X-RAY DIFFRACTIONr_chiral_restr0.0680.2296
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022074
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02427
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A39660.17
12B39660.17
21A36020.18
22C36020.18
31B39050.17
32C39050.17
LS refinement shellResolution: 2.875→3.03 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.452 40 -
Rwork0.331 882 -
obs--95.15 %

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