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- PDB-6se5: Y830A mutant from Mycoplasma genitalium P110 adhesin -

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Basic information

Entry
Database: PDB / ID: 6se5
TitleY830A mutant from Mycoplasma genitalium P110 adhesin
ComponentsMgp-operon protein 3
KeywordsSUGAR BINDING PROTEIN / Adhesion complex
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: 2.21 Å
AuthorsFita, I. / Aparicio, D.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesMDM-2014-0435 Spain
CitationJournal: To Be Published
Title: Mycoplasma genitalium complex
Authors: Fita, I. / Aparicio, D.
History
DepositionJul 29, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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

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Assembly

Deposited unit
A: Mgp-operon protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4182
Polymers100,3791
Non-polymers391
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-0 kcal/mol
Surface area34250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.322, 153.117, 169.902
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

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


Mass: 100379.078 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 BL21(DE3) (bacteria) / 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.: 291 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.69 Å3/Da / Density % sol: 66.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 23 % PEG 3350 0.2 M Tri-potassium citrate

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Data collection

DiffractionMean temperature: 98 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.21→91.93 Å / Num. obs: 70593 / % possible obs: 98.8 % / Redundancy: 4.6 % / CC1/2: 0.99 / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.5
Reflection shellResolution: 2.21→2.24 Å / Rmerge(I) obs: 1.55 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 3502 / CC1/2: 0.49 / % possible all: 99

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6R3T

6r3t


Resolution: 2.21→32.3 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.919 / SU R Cruickshank DPI: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.174 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.227 3570 5.06 %RANDOM
Rwork0.192 ---
obs0.194 70569 98.8 %-
Displacement parametersBiso max: 213.96 Å2 / Biso mean: 85.63 Å2 / Biso min: 50.3 Å2
Baniso -1Baniso -2Baniso -3
1-28.0684 Å20 Å20 Å2
2---14.8635 Å20 Å2
3----13.205 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: final / Resolution: 2.21→32.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6807 0 1 291 7099
Biso mean--58.63 76.24 -
Num. residues----885
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2347SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1197HARMONIC5
X-RAY DIFFRACTIONt_it6952HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion951SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7867SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6952HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9458HARMONIC21.22
X-RAY DIFFRACTIONt_omega_torsion3.12
X-RAY DIFFRACTIONt_other_torsion19.92
LS refinement shellResolution: 2.21→2.23 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2945 72 5.1 %
Rwork0.2946 1340 -
all0.2946 1412 -
obs--98.89 %
Refinement TLS params.Method: refined / Origin x: 8.6155 Å / Origin y: 31.9443 Å / Origin z: 48.2728 Å
111213212223313233
T-0.2047 Å2-0.054 Å2-0.0238 Å2--0.0509 Å20.2261 Å2--0.2637 Å2
L0.6918 °2-0.1191 °2-0.01 °2-0.6951 °2-0.3328 °2--0.5449 °2
S-0.0475 Å °0.1845 Å °0.4145 Å °0.0254 Å °-0.0672 Å °-0.1825 Å °-0.0023 Å °-0.0227 Å °0.1148 Å °
Refinement TLS groupSelection details: { A|* }

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