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- PDB-5ox7: Structure of P110 from Mycoplasma genitalium at 2.4A with potassi... -

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Basic information

Entry
Database: PDB / ID: 5ox7
TitleStructure of P110 from Mycoplasma genitalium at 2.4A with potassium ion
ComponentsMgp-operon protein 3
KeywordsCELL ADHESION / Mycoplasma genitalium protein D
Function / homologyMgpC adhesin / Mgp-operon protein 3, C-terminal domain / MgpC adhesin / MGP3 C-terminal domain / cell adhesion / plasma membrane / : / Mgp-operon protein 3
Function and homology information
Biological speciesMycoplasma genitalium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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
DepositionSep 6, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2018Group: Data collection / Structure summary / Category: struct / Item: _struct.title
Revision 1.2Nov 7, 2018Group: Data collection / Database references / Structure summary
Category: citation / citation_author / entity
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity.formula_weight
Revision 1.3Jan 17, 2024Group: 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: Mgp-operon protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5942
Polymers99,5551
Non-polymers391
Water2,036113
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-0 kcal/mol
Surface area34700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.603, 151.293, 176.245
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 (strain ATCC 33530 / G-37 / NCTC 10195) (bacteria)
Strain: ATCC 33530 / G-37 / NCTC 10195 / Gene: MG192 / Production host: Escherichia coli (E. coli) / Strain (production host): B836 / References: UniProt: P22747
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 3.67 Å3/Da / Density % sol: 66.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350 21% 0.2M Tri-potassium citrate

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Data collection

DiffractionMean temperature: 78 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97895 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.4→62.54 Å / Num. obs: 56936 / % possible obs: 99.6 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 15.3
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 1.8 / Num. measured obs: 28274 / Num. unique all: 8248 / CC1/2: 0.706 / Rpim(I) all: 0.469 / Rrim(I) all: 0.877 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MZB

5mzb
PDB Unreleased entry


Resolution: 2.4→62.54 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 18.797 / SU ML: 0.202 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.21 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23971 2770 4.9 %RANDOM
Rwork0.19129 ---
obs0.19363 54151 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 74.37 Å2
Baniso -1Baniso -2Baniso -3
1--2.68 Å20 Å20 Å2
2--1.62 Å20 Å2
3---1.07 Å2
Refinement stepCycle: 1 / Resolution: 2.4→62.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6818 0 1 113 6932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.026964
X-RAY DIFFRACTIONr_bond_other_d0.0020.026149
X-RAY DIFFRACTIONr_angle_refined_deg2.371.9419472
X-RAY DIFFRACTIONr_angle_other_deg1.31314390
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0795884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.72325.949316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.702151135
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7221518
X-RAY DIFFRACTIONr_chiral_restr0.1430.21079
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217842
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021340
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_it3.94.8923548
X-RAY DIFFRACTIONr_mcbond_other3.8944.8913547
X-RAY DIFFRACTIONr_mcangle_it6.2677.3134428
X-RAY DIFFRACTIONr_mcangle_other6.2667.3144429
X-RAY DIFFRACTIONr_scbond_it3.8435.0813416
X-RAY DIFFRACTIONr_scbond_other3.8435.0823417
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9897.4795044
X-RAY DIFFRACTIONr_long_range_B_refined8.91656.3127525
X-RAY DIFFRACTIONr_long_range_B_other8.91956.2717504
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.404→2.467 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 213 -
Rwork0.355 3967 -
obs--99.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5135-0.08020.21780.7588-0.60670.784-0.17010.21950.23910.06110.0159-0.2730.0507-0.16140.15420.1306-0.1539-0.1160.33480.26650.36877.6278188.556945.7482
20.4136-0.3150.02430.7255-0.50210.698-0.14710.0535-0.0174-0.0388-0.0397-0.03360.0450.12450.18680.231-0.04360.04340.21330.04110.217418.6415146.928578.9216
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 812
2X-RAY DIFFRACTION2A813 - 936

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