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- PDB-4xng: Central Domain of Mycoplasma Genitalium Terminal Organelle protei... -

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Basic information

Entry
Database: PDB / ID: 4xng
TitleCentral Domain of Mycoplasma Genitalium Terminal Organelle protein MG491
ComponentsUncharacterized protein MG218.1
KeywordsUNKNOWN FUNCTION / antiparallel three-helix bundles / asymmetric dimer of dimers / gliding motility
Function / homology: / Organelle protein MG491, central domain / Uncharacterized protein MG218.1
Function and homology information
Biological speciesMycoplasma genitalium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsMartinelli, L. / Fita, I.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e InnovacionBFU2012-36827 Spain
CitationJournal: Plos Pathog. / Year: 2016
Title: Structure-Guided Mutations in the Terminal Organelle Protein MG491 Cause Major Motility and Morphologic Alterations on Mycoplasma genitalium.
Authors: Martinelli, L. / Garcia-Morales, L. / Querol, E. / Pinol, J. / Fita, I. / Calisto, B.M.
History
DepositionJan 15, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein MG218.1
B: Uncharacterized protein MG218.1
C: Uncharacterized protein MG218.1
D: Uncharacterized protein MG218.1


Theoretical massNumber of molelcules
Total (without water)67,0804
Polymers67,0804
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7330 Å2
ΔGint-25 kcal/mol
Surface area28170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.270, 108.420, 62.190
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNALAALAAA67 - 2036 - 142
21ASNASNGLUGLUBB67 - 2026 - 141
12HISHISGLUGLUAA66 - 2025 - 141
22HISHISGLUGLUCC66 - 2025 - 141
13PHEPHEALAALAAA65 - 2034 - 142
23PHEPHEALAALADD65 - 2034 - 142
14ASNASNGLUGLUBB67 - 2026 - 141
24ASNASNGLUGLUCC67 - 2026 - 141
15ASNASNGLUGLUBB67 - 2026 - 141
25ASNASNALAALADD67 - 2036 - 142
16HISHISGLUGLUCC66 - 2025 - 141
26HISHISGLUGLUDD66 - 2025 - 141

NCS ensembles :
ID
1
2
3
4
5
6
Detailsbiological unit is the same as asym.

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Components

#1: Protein
Uncharacterized protein MG218.1


Mass: 16769.986 Da / Num. of mol.: 4 / Fragment: UNP residues 63-204 / Mutation: I168M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma genitalium (bacteria) / Gene: MG218.1 / Plasmid: pOPINE / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9ZB78
Has protein modificationY

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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: 1.94 Å3/Da / Density % sol: 36.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG3350, Li2SO4, Tris / PH range: 7.5 - 8.5

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryogenic data collection
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979154 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 31, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979154 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 13879 / % possible obs: 95.3 % / Observed criterion σ(I): 2 / Redundancy: 19.5 % / Rmerge(I) obs: 0.199 / Net I/σ(I): 10.6
Reflection shellResolution: 3→3.16 Å / Redundancy: 20.2 % / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / SU B: 50.093 / SU ML: 0.398 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.467 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 667 5 %RANDOM
Rwork0.2258 12541 --
obs0.227 13851 95.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 214.77 Å2 / Biso mean: 87.896 Å2 / Biso min: 37.93 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å2-0 Å20 Å2
2--1.16 Å2-0 Å2
3---0.71 Å2
Refinement stepCycle: final / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4588 0 0 0 4588
Num. residues----559
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194653
X-RAY DIFFRACTIONr_bond_other_d0.0060.024613
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9876240
X-RAY DIFFRACTIONr_angle_other_deg1.195310634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9275555
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.08625.212236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.59415933
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2551528
X-RAY DIFFRACTIONr_chiral_restr0.0730.2707
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025189
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021065
X-RAY DIFFRACTIONr_mcbond_it2.3183.8692232
X-RAY DIFFRACTIONr_mcbond_other2.3193.8692231
X-RAY DIFFRACTIONr_mcangle_it3.7595.8082783
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A84050.09
12B84050.09
21A85850.08
22C85850.08
31A85950.09
32D85950.09
41B84240.1
42C84240.1
51B86690.07
52D86690.07
61C85020.1
62D85020.1
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 40 -
Rwork0.313 578 -
all-618 -
obs--62.68 %
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)
120.668610.065-12.526443.290710.217714.5432-0.74320.55941.4810.83671.89370.32461.00360.4048-1.15050.80180.0524-0.29840.50940.0441.062-12.11548.411-8.991
28.25744.87151.3738.5380.48872.7918-0.19620.60010.1044-0.42140.4101-0.07140.1421-0.2386-0.21380.301-0.00460.02960.09240.04260.0326-17.33925.396-0.19
3116.7692-31.07726.893722.9048-2.25256.2823-2.2199-1.64978.3065-0.32781.01741.41591.9388-1.92051.20261.26960.1643-0.10010.25360.20261.7839-52.82841.45410.486
43.5723-0.48240.24158.3588-3.64227.0893-0.0466-0.2875-0.23630.25410.1216-0.0911-0.3079-0.2665-0.0750.13-0.04840.00530.21810.11650.1994-40.58217.30211.902
544.298644.5606-15.446383.2715-10.15166.1416-1.15311.3905-2.39191.1997-0.45513.09640.7626-0.71741.60821.23480.280.31781.2722-0.22051.1539-46.07250.53837.233
69.7276-6.00850.00768.55570.43492.3612-0.1112-1.34740.56740.59050.4748-0.3107-0.0230.261-0.36360.47530.00750.03540.80910.03450.1394-39.61625.25430.997
782.3363-22.482634.614216.932-17.257220.2204-2.78394.90784.25921.2372-1.0586-3.8525-1.40731.86593.84241.5794-0.48150.28380.6976-0.04741.59-5.08941.01619.81
84.55762.43840.23929.30633.92566.99140.0878-0.4983-0.41940.29690.2333-0.1431-0.10130.1066-0.32110.12920.0213-0.06680.09170.06710.2146-16.16917.53418.531
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1D62 - 70
2X-RAY DIFFRACTION2D71 - 205
3X-RAY DIFFRACTION3C65 - 70
4X-RAY DIFFRACTION4C71 - 205
5X-RAY DIFFRACTION5B65 - 70
6X-RAY DIFFRACTION6B71 - 205
7X-RAY DIFFRACTION7A65 - 70
8X-RAY DIFFRACTION8A71 - 205

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