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Basic information

Entry
Database: PDB / ID: 6hjm
TitleMyxococcus xanthus MglB
ComponentsMglB
KeywordsCYTOSOLIC PROTEIN / Small GTPase / guanyl-nucleotide exchange factor (GEF)
Function / homologyRagulator complex protein LAMTOR2-like / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / positive regulation of TOR signaling / guanyl-nucleotide exchange factor activity / molecular adaptor activity / Dynein regulation protein LC7
Function and homology information
Biological speciesMyxococcus xanthus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsVarela, P.F. / Navaza, J. / Trapani, S. / Cherfils, J.
CitationJournal: Nat Commun / Year: 2019
Title: MglA functions as a three-state GTPase to control movement reversals of Myxococcus xanthus.
Authors: Galicia, C. / Lhospice, S. / Varela, P.F. / Trapani, S. / Zhang, W. / Navaza, J. / Herrou, J. / Mignot, T. / Cherfils, J.
History
DepositionSep 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 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

Downloads & links

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Assembly

Deposited unit
A: MglB
B: MglB
E: MglB
F: MglB
C: MglB
D: MglB
G: MglB
H: MglB
I: MglB
J: MglB
M: MglB
N: MglB
Q: MglB
R: MglB
K: MglB
L: MglB
O: MglB
P: MglB
S: MglB
T: MglB


Theoretical massNumber of molelcules
Total (without water)412,62520
Polymers412,62520
Non-polymers00
Water5,278293
1
A: MglB
B: MglB


Theoretical massNumber of molelcules
Total (without water)41,2622
Polymers41,2622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-24 kcal/mol
Surface area12910 Å2
MethodPISA
2
E: MglB
F: MglB


Theoretical massNumber of molelcules
Total (without water)41,2622
Polymers41,2622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2500 Å2
ΔGint-23 kcal/mol
Surface area12530 Å2
MethodPISA
3
C: MglB
D: MglB


Theoretical massNumber of molelcules
Total (without water)41,2622
Polymers41,2622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2530 Å2
ΔGint-24 kcal/mol
Surface area12130 Å2
MethodPISA
4
G: MglB
H: MglB


Theoretical massNumber of molelcules
Total (without water)41,2622
Polymers41,2622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-24 kcal/mol
Surface area12100 Å2
MethodPISA
5
I: MglB
J: MglB


Theoretical massNumber of molelcules
Total (without water)41,2622
Polymers41,2622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-25 kcal/mol
Surface area12600 Å2
MethodPISA
6
M: MglB
N: MglB


Theoretical massNumber of molelcules
Total (without water)41,2622
Polymers41,2622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-23 kcal/mol
Surface area12290 Å2
MethodPISA
7
Q: MglB
R: MglB


Theoretical massNumber of molelcules
Total (without water)41,2622
Polymers41,2622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-24 kcal/mol
Surface area12540 Å2
MethodPISA
8
K: MglB
L: MglB


Theoretical massNumber of molelcules
Total (without water)41,2622
Polymers41,2622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-24 kcal/mol
Surface area12180 Å2
MethodPISA
9
O: MglB
P: MglB


Theoretical massNumber of molelcules
Total (without water)41,2622
Polymers41,2622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-24 kcal/mol
Surface area13200 Å2
MethodPISA
10
S: MglB
T: MglB


Theoretical massNumber of molelcules
Total (without water)41,2622
Polymers41,2622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-24 kcal/mol
Surface area12860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.783, 139.599, 179.416
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
MglB


Mass: 20631.244 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myxococcus xanthus (bacteria) / Gene: mglB / Production host: Escherichia coli (E. coli) / References: UniProt: Q50883
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.1M MES, 0.15M Ammonium sulphate, 15% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.39→45.41 Å / Num. obs: 118348 / % possible obs: 73 % / Redundancy: 9 % / Biso Wilson estimate: 52.45 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08658 / Rrim(I) all: 0.09194 / Net I/σ(I): 15.36
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.925 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1124 / Rrim(I) all: 2.043 / % possible all: 97

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
XSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3T1S

3t1s


Resolution: 2.39→45.41 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.889 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.95 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.876 / SU Rfree Blow DPI: 0.326 / SU Rfree Cruickshank DPI: 0.335
RfactorNum. reflection% reflectionSelection details
Rfree0.267 4276 4.93 %RANDOM
Rwork0.249 ---
obs0.25 86658 72.6 %-
Displacement parametersBiso mean: 70.48 Å2
Baniso -1Baniso -2Baniso -3
1--1.3508 Å20 Å20 Å2
2--1.6689 Å20 Å2
3----0.3181 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: 1 / Resolution: 2.39→45.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19033 0 0 293 19326
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00819206HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.125881HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6972SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes530HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2753HARMONIC5
X-RAY DIFFRACTIONt_it19206HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.1
X-RAY DIFFRACTIONt_other_torsion20.76
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2653SEMIHARMONIC5
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_contact22034SEMIHARMONIC4
LS refinement shellResolution: 2.39→2.45 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 -4.79 %
Rwork0.237 636 -
all0.238 668 -
obs--7.63 %
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)
13.5834-1.7088-0.03994.0381-0.32132.18930.10870.28870.2244-0.4001-0.15090.0523-0.0942-0.22240.04220.00470.02990.03540.0067-0.0415-0.212350.0498182.596258.968
22.84350.4210.20392.00731.34141.63720.06140.17760.16140.0551-0.1457-0.261-0.0270.28490.0843-0.18670.0076-0.0512-0.13570.13030.013380.6341186.729222.907
32.9242.57120.22416.1033-1.99145.1090.0831-0.2178-0.43210.0777-0.00790.32210.4897-0.2609-0.0752-0.0015-0.16820.01320.1025-0.12960.041881.0339125.398249.748
44.3863-1.23141.6392.5643-0.44551.98010.0255-0.35410.03150.0827-0.04810.0525-0.1407-0.39050.0226-0.19970.0267-0.0076-0.07260.0085-0.117556.4608194.623227.668
53.49111.24390.60913.57210.46774.69180.0144-0.05770.22190.0169-0.1523-0.01540.21550.16350.1379-0.1964-0.0716-0.002-0.0549-0.1821-0.077989.4426138.328231.36
64.4945-2.3996-0.75093.72711.14282.5309-0.0959-0.1658-0.36280.4870.14420.01630.2350.3557-0.0483-0.11130.04990.1124-0.04880.04360.1617122.796156.486224.658
71.52961.2452-1.01067.90241.48740.87690.0506-0.23260.34210.0975-0.1157-0.2275-0.41590.18540.06510.2263-0.1385-0.1790.0812-0.10970.377499.3599226.351253.932
88.27570.4648-0.14524.5624-1.47521.9321-0.04060.0403-0.58550.0684-0.19420.42330.0964-0.11610.2348-0.23350.0240.1324-0.1658-0.06840.130199.2461165.031221.415
91.34370.78260.75131.7347-1.48854.0386-0.04550.05910.4196-0.0306-0.03250.0209-0.1868-0.11060.0779-0.2297-0.02390.0573-0.14520.06820.173488.8582213.381234.884
104.1120.43560.45444.6531-1.17733.6989-0.01560.037-0.13970.11310.02170.16440.0841-0.2576-0.006-0.1637-0.0142-0.0364-0.1699-0.0823-0.081256.2613164.338226.725
113.22180.9838-0.00013.42240.87842.79450.1248-0.43590.32810.3733-0.0193-0.2156-0.09810.1178-0.10550.0182-0.12910.00150.1893-0.0528-0.165371.6713182.345281.226
121.34991.47210.02141.87091.50785.3087-0.00490.5669-0.1657-0.5843-0.1098-0.00090.2274-0.09530.11470.07820.0507-0.0180.0793-0.0891-0.038262.4048172.122204.259
132.2998-1.8860.06543.0892-1.87813.05970.06660.50010.4402-0.3772-0.02450.00270.2794-0.1386-0.0421-0.04810.0696-0.0160.20780.1282-0.1604116.306187.052254.185
144.40421.75210.51115.7071.82915.6597-0.09870.10420.377-0.02490.1521-0.181-0.31530.6077-0.0534-0.0274-0.15620.01970.0710.1857-0.0981123.949187.015225.424
150.38811.31230.07832.755-2.65437.60630.01580.5890.1048-0.3448-0.29840.0956-0.38470.42970.28260.082-0.04730.00040.40410.2166-0.0554116.752180.33202.696
166.9756-1.6272-0.90552.78393.10015.1355-0.1154-0.09840.28150.09880.12120.0837-0.4276-0.0948-0.0058-0.08410.0617-0.1012-0.1281-0.0946-0.159290.4664151.141261.777
176.7186-1.08820.36572.29240.84623.0831-0.04860.33740.08740.24850.1335-0.31640.13080.5456-0.0849-0.11980.0231-0.11070.1565-0.2565-0.0664111.032138.33253.578
185.50.05010.6082.8697-0.46424.941-0.121-0.56390.0980.21640.1123-0.21090.2223-0.22340.0087-0.07340.00870.0591-0.0711-0.0969-0.162891.2569197.61264.029
193.6333-1.5081-0.46953.2041-0.89112.951-0.0798-0.21230.34820.40890.06190.4336-0.1881-0.56330.0179-0.09450.01960.13190.1705-0.15690.177370.482210.13257.079
202.8617-1.4366-0.10014.45521.54244.25410.16010.5996-0.6017-0.4076-0.14620.0597-0.03290.3974-0.0139-0.07410.0663-0.01880.0652-0.1023-0.142264.8377162.764255.574
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ N|10 - N|132 }
2X-RAY DIFFRACTION2{ A|6 - A|133 }
3X-RAY DIFFRACTION3{ O|12 - O|130 }
4X-RAY DIFFRACTION4{ B|8 - B|133 }
5X-RAY DIFFRACTION5{ P|8 - P|132 }
6X-RAY DIFFRACTION6{ C|6 - C|131 }
7X-RAY DIFFRACTION7{ Q|10 - Q|131 }
8X-RAY DIFFRACTION8{ D|12 - D|131 }
9X-RAY DIFFRACTION9{ R|7 - R|131 }
10X-RAY DIFFRACTION10{ E|10 - E|132 }
11X-RAY DIFFRACTION11{ S|5 - S|131 }
12X-RAY DIFFRACTION12{ F|12 - F|131 }
13X-RAY DIFFRACTION13{ T|6 - T|131 }
14X-RAY DIFFRACTION14{ G|6 - G|131 }
15X-RAY DIFFRACTION15{ H|11 - H|131 }
16X-RAY DIFFRACTION16{ I|7 - I|133 }
17X-RAY DIFFRACTION17{ J|7 - J|130 }
18X-RAY DIFFRACTION18{ K|12 - K|130 }
19X-RAY DIFFRACTION19{ L|10 - L|132 }
20X-RAY DIFFRACTION20{ M|9 - M|133 }

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