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- PDB-6se7: R600A mutant from Mycoplasma genitalium P110 Adhesin at 1.87 Angs... -

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Basic information

Entry
Database: PDB / ID: 6se7
TitleR600A mutant from Mycoplasma genitalium P110 Adhesin at 1.87 Angstroms resolution
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: 1.87 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: R600A mutant from Mycoplasma genitalium P110 Adhesin at 1.87 Angstroms resolution
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)100,5102
Polymers100,4711
Non-polymers391
Water12,611700
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-0 kcal/mol
Surface area34450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.393, 150.696, 176.221
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1262-

HOH

21A-1324-

HOH

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Components

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


Mass: 100471.172 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.: 700 / 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: 3.76 Å3/Da / Density % sol: 67.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 25% PEG 3350 0.2M 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: 1.87→88.52 Å / Num. obs: 73762 / % possible obs: 61.5 % / Redundancy: 4.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.039 / Net I/σ(I): 16.3
Reflection shellResolution: 1.87→2.08 Å / Rmerge(I) obs: 0.73 / Mean I/σ(I) obs: 2 / Num. unique obs: 3689 / CC1/2: 0.75

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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: 1.87→27.36 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU R Cruickshank DPI: 0.157 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.165 / SU Rfree Blow DPI: 0.148 / SU Rfree Cruickshank DPI: 0.145
RfactorNum. reflection% reflectionSelection details
Rfree0.207 3689 5 %RANDOM
Rwork0.172 ---
obs0.174 73718 61.5 %-
Displacement parametersBiso max: 200.28 Å2 / Biso mean: 60.32 Å2 / Biso min: 23.76 Å2
Baniso -1Baniso -2Baniso -3
1--1.1401 Å20 Å20 Å2
2--0.6805 Å20 Å2
3---0.4596 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 1.87→27.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6814 0 1 704 7519
Biso mean--32.45 58.23 -
Num. residues----885
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2345SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1195HARMONIC5
X-RAY DIFFRACTIONt_it6954HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion950SEMIHARMONIC5
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_contact8176SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6954HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9459HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion19.11
LS refinement shellResolution: 1.87→2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.252 62 4.2 %
Rwork0.2187 1413 -
all0.2201 1475 -
obs--6.6 %
Refinement TLS params.Method: refined / Origin x: 9.2425 Å / Origin y: 31.3533 Å / Origin z: 50.2443 Å
111213212223313233
T-0.1767 Å2-0.0856 Å2-0.0424 Å2-0.0898 Å20.2559 Å2--0.0264 Å2
L0.8867 °2-0.2201 °20.0762 °2-1.0028 °2-0.6915 °2--1.0957 °2
S-0.0857 Å °0.4284 Å °0.4103 Å °-0.0385 Å °-0.0461 Å °-0.2005 Å °-0.0511 Å °-0.0434 Å °0.1317 Å °
Refinement TLS groupSelection details: { A|* }

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