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- PDB-6rcc: Domain C P140 Mycoplasma genitalium -

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Basic information

Entry
Database: PDB / ID: 6rcc
TitleDomain C P140 Mycoplasma genitalium
ComponentsAdhesin P1
KeywordsCELL ADHESION / extracellular
Function / homologyAdhesin P1, C-terminal domain / Adhesin P1, N-terminal / Adhesin P1 / Mycoplasma adhesin P1, C-terminal / Mycoplasma adhesin P1, N-terminal / adhesion of symbiont to microvasculature / plasma membrane / Adhesin P1
Function and homology information
Biological speciesMycoplasma genitalium G37 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.43 Å
AuthorsVizarraga, D. / Aparicio, D. / Perez, R. / Illanes, R. / Fita, I.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Economy and Competitiveness Spain
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: Alternative conformation of the C-domain of the P140 protein from Mycoplasma genitalium.
Authors: Vizarraga, D. / Perez-Luque, R. / Martin, J. / Fita, I. / Aparicio, D.
History
DepositionApr 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Structure summary / Category: citation / struct
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct.title
Revision 1.2May 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
X: Adhesin P1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5943
Polymers11,5361
Non-polymers582
Water2,252125
1
X: Adhesin P1
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)92,75524
Polymers92,2888
Non-polymers46816
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_656-x+1,y,-z+11
crystal symmetry operation6_566x,-y+1,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area31330 Å2
ΔGint-462 kcal/mol
Surface area32820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.090, 90.090, 58.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11X-201-

NA

21X-308-

HOH

31X-395-

HOH

41X-399-

HOH

51X-410-

HOH

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Components

#1: Protein Adhesin P1 / Attachment protein / Cytadhesin P1 / MgPa


Mass: 11535.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium G37 (bacteria) / Gene: mgpA, MG191 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P20796
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.55 Å3/Da / Density % sol: 51.8 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: PEG3350, mgCl2 x 6H20 and TRIS buffer

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.07216 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07216 Å / Relative weight: 1
ReflectionResolution: 1.43→45.04 Å / Num. obs: 20650 / % possible obs: 92.41 % / Redundancy: 6.3 % / Biso Wilson estimate: 22.25 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.5
Reflection shellResolution: 1.43→1.51 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
SHELXDEphasing
RefinementMethod to determine structure: MIR / Resolution: 1.43→45.04 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.959 / SU R Cruickshank DPI: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.07 / SU Rfree Blow DPI: 0.067 / SU Rfree Cruickshank DPI: 0.064
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1055 5.11 %RANDOM
Rwork0.183 ---
obs0.184 20650 92.4 %-
Displacement parametersBiso mean: 29.94 Å2
Baniso -1Baniso -2Baniso -3
1--2.8345 Å20 Å20 Å2
2---2.8345 Å20 Å2
3---5.6691 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: 1 / Resolution: 1.43→45.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms798 0 2 125 925
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01887HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.11222HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d302SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes157HARMONIC5
X-RAY DIFFRACTIONt_it887HARMONIC20
X-RAY DIFFRACTIONt_nbd6SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.11
X-RAY DIFFRACTIONt_other_torsion16.13
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion114SEMIHARMONIC5
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_contact1131SEMIHARMONIC4
LS refinement shellResolution: 1.43→1.51 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.2687 162 5.1 %
Rwork0.2384 3012 -
all0.2398 3174 -
obs--99.35 %
Refinement TLS params.Method: refined / Origin x: 56.7773 Å / Origin y: 34.3883 Å / Origin z: 15.636 Å
111213212223313233
T0.0086 Å2-0.0008 Å20.01 Å2-0.0123 Å2-0.0078 Å2--0.0076 Å2
L0.4682 °2-0.0182 °2-0.2549 °2-0.126 °2-0.1317 °2--0.3185 °2
S0.0332 Å °0.0409 Å °0.0227 Å °-0.032 Å °-0.0434 Å °-0.0043 Å °-0.0212 Å °-0.0054 Å °0.0102 Å °
Refinement TLS groupSelection details: { X|* }

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