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- PDB-7cy1: Crystal Structure of MglC from Myxococcus xanthus -

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Basic information

Entry
Database: PDB / ID: 7cy1
TitleCrystal Structure of MglC from Myxococcus xanthus
ComponentsMutual gliding motility protein C
KeywordsCYTOSOLIC PROTEIN / Roadblock/LC7 domain
Function / homologyDynein light chain 2a, cytoplasmic / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta / GTPase
Function and homology information
Biological speciesMyxococcus xanthus DK 1622 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsThakur, K.G. / Kapoor, S. / Kodesia, A.
Funding support India, 1items
OrganizationGrant numberCountry
Council of Scientific & Industrial Research (CSIR) India
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural characterization of Myxococcus xanthus MglC, a component of the polarity control system, and its interactions with its paralog MglB.
Authors: Kapoor, S. / Kodesia, A. / Kalidas, N. / Thakur, K.G.
History
DepositionSep 3, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.2May 1, 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
A: Mutual gliding motility protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1582
Polymers13,1351
Non-polymers231
Water72140
1
A: Mutual gliding motility protein C
hetero molecules

A: Mutual gliding motility protein C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3164
Polymers26,2702
Non-polymers462
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/31
Buried area1830 Å2
ΔGint-30 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.910, 96.910, 58.050
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Mutual gliding motility protein C


Mass: 13134.907 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus DK 1622 (bacteria) / Strain: DK 1622 / Gene: MXAN_5770 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1D0B6
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.91 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.8 M Sodium Acetate Trihydrate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 26, 2020 / Details: LN2 closed loop cooling
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.19→27.98 Å / Num. obs: 8534 / % possible obs: 98.8 % / Redundancy: 18.1 % / CC1/2: 1 / Rmerge(I) obs: 0.075 / Net I/σ(I): 26.1 / Num. measured all: 154682 / Scaling rejects: 292
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
2.19-2.2615.80.959111597080.8853.997.2
9.04-27.9813.70.0252076151169.595.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
iMOSFLM7.2.2data reduction
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CT3

7ct3


Resolution: 2.19→27.98 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.911 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2269 465 5.5 %RANDOM
Rwork0.1882 ---
obs0.1904 8065 98.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 142.17 Å2 / Biso mean: 46.966 Å2 / Biso min: 28.34 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.27 Å2-0 Å2
2---0.54 Å20 Å2
3---1.75 Å2
Refinement stepCycle: final / Resolution: 2.19→27.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms921 0 1 40 962
Biso mean--45.21 55.32 -
Num. residues----120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.013934
X-RAY DIFFRACTIONr_bond_other_d0.0010.017884
X-RAY DIFFRACTIONr_angle_refined_deg1.4621.631266
X-RAY DIFFRACTIONr_angle_other_deg1.3291.5732039
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.65119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11922.55347
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92215160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.189156
X-RAY DIFFRACTIONr_chiral_restr0.0670.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021048
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02194
LS refinement shellResolution: 2.192→2.249 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 35 -
Rwork0.311 565 -
all-600 -
obs--95.85 %

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