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- PDB-6r3t: Structure of P110 from Mycoplasma Genitalium at 2.7A -

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Basic information

Entry
Database: PDB / ID: 6r3t
TitleStructure of P110 from Mycoplasma Genitalium at 2.7A
ComponentsMgp-operon protein 3
KeywordsSUGAR BINDING PROTEIN / Adhesin
Function / homologyMgpC adhesin / Mgp-operon protein 3, C-terminal domain / MgpC adhesin / MGP3 C-terminal domain / cell adhesion / plasma membrane / : / PHOSPHATE ION / Mgp-operon protein 3
Function and homology information
Biological speciesMycoplasma genitalium G37 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.73 Å
AuthorsAparicio, D. / Fita, I.
CitationJournal: Nat Commun / Year: 2018
Title: Mycoplasma genitalium adhesin P110 binds sialic-acid human receptors.
Authors: Aparicio, D. / Torres-Puig, S. / Ratera, M. / Querol, E. / Pinol, J. / Pich, O.Q. / Fita, I.
History
DepositionMar 21, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionApr 10, 2019ID: 5MZB
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 1.1May 15, 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: Mgp-operon protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,7284
Polymers99,5551
Non-polymers1733
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area620 Å2
ΔGint-6 kcal/mol
Surface area34890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.600, 152.940, 172.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Mgp-operon protein 3 / Mgp3 / ORF-3 protein


Mass: 99555.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium G37 (bacteria) / Gene: MG192 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P22747
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 3.6 Å3/Da / Density % sol: 65.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 11% PEG 8000 0.1M Imidazole pH 8 0.2M Calcium acetate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.12712 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.12712 Å / Relative weight: 1
ReflectionResolution: 2.7→62 Å / Num. obs: 39641 / % possible obs: 98.9 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.047 / Rpim(I) all: 0.052 / Net I/σ(I): 19.1
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 4.8 % / Num. unique obs: 39641

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.73→54.86 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.941 / SU B: 27.881 / SU ML: 0.254 / Cross valid method: THROUGHOUT / ESU R: 0.433 / ESU R Free: 0.273 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 1930 5 %RANDOM
Rwork0.17593 ---
obs0.17836 36543 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 89.398 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å2-0 Å2
2--0.04 Å20 Å2
3----0.94 Å2
Refinement stepCycle: 1 / Resolution: 2.73→54.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6825 0 7 63 6895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0136980
X-RAY DIFFRACTIONr_bond_other_d0.0040.0176174
X-RAY DIFFRACTIONr_angle_refined_deg1.9321.6419495
X-RAY DIFFRACTIONr_angle_other_deg1.3371.57314447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.1935884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.58524.955335
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.567151137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0491519
X-RAY DIFFRACTIONr_chiral_restr0.0790.2957
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027867
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021366
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_it2.9234.7793548
X-RAY DIFFRACTIONr_mcbond_other2.9134.7783547
X-RAY DIFFRACTIONr_mcangle_it4.6377.1624428
X-RAY DIFFRACTIONr_mcangle_other4.6377.1634429
X-RAY DIFFRACTIONr_scbond_it3.2264.9833432
X-RAY DIFFRACTIONr_scbond_other3.1774.983429
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.9777.365062
X-RAY DIFFRACTIONr_long_range_B_refined7.35155.2477444
X-RAY DIFFRACTIONr_long_range_B_other7.3455.1937436
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.727→2.798 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 164 -
Rwork0.324 2628 -
obs--98.66 %
Refinement TLS params.Method: refined / Origin x: 8.9538 Å / Origin y: 184.6664 Å / Origin z: 49.2386 Å
111213212223313233
T0.1355 Å2-0.1328 Å2-0.0925 Å2-0.3662 Å20.3948 Å2--0.539 Å2
L1.1178 °2-0.5229 °20.1774 °2-2.7155 °2-1.7506 °2--2.1965 °2
S-0.0933 Å °0.5228 Å °0.5621 Å °-0.1988 Å °-0.0658 Å °-0.2922 Å °0.0271 Å °-0.0775 Å °0.1591 Å °

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