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- PDB-4z29: Crystal structure of the magnetobacterial protein MtxA C-terminal... -

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Basic information

Entry
Database: PDB / ID: 4z29
TitleCrystal structure of the magnetobacterial protein MtxA C-terminal domain
ComponentsMagnetotaxis protein MtxA
KeywordsSIGNALING PROTEIN / MtxA / TPR / Big
Function / homologyMagnetotaxis protein MtxA
Function and homology information
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å
AuthorsZarivach, R. / Davidov, G.
CitationJournal: Front Mol Biosci / Year: 2015
Title: Crystal structure of the magnetobacterial protein MtxA C-terminal domain reveals a new sequence-structure relationship.
Authors: Davidov, G. / Muller, F.D. / Baumgartner, J. / Bitton, R. / Faivre, D. / Schuler, D. / Zarivach, R.
History
DepositionMar 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Magnetotaxis protein MtxA
B: Magnetotaxis protein MtxA


Theoretical massNumber of molelcules
Total (without water)69,6442
Polymers69,6442
Non-polymers00
Water2,522140
1
A: Magnetotaxis protein MtxA


Theoretical massNumber of molelcules
Total (without water)34,8221
Polymers34,8221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Magnetotaxis protein MtxA


Theoretical massNumber of molelcules
Total (without water)34,8221
Polymers34,8221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.344, 88.954, 95.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A137 - 304
2010B137 - 304

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Components

#1: Protein Magnetotaxis protein MtxA


Mass: 34821.816 Da / Num. of mol.: 2 / Fragment: C-terminal domain, UNP residues 25-313
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic)
Gene: mtxA, MGR_0208 / Plasmid: pET-51b(+)Ek/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A4TUL6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / 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: 286 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M sodium malonate pH 7.0, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.03→50 Å / Num. obs: 22793 / % possible obs: 99.2 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.143 / Χ2: 6.753 / Net I/av σ(I): 44.316 / Net I/σ(I): 12.4 / Num. measured all: 266426
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.03-2.074.90.65910003.64991.3
2.07-2.15.70.60910753.18594.5
2.1-2.146.40.59111102.81498.2
2.14-2.197.20.51311084.95899.7
2.19-2.238.40.44211473.753100
2.23-2.299.80.44311225.711100
2.29-2.3412.40.42311304.906100
2.34-2.4113.80.40211407.767100
2.41-2.48140.34411276.614100
2.48-2.5614.10.32311458.409100
2.56-2.6514.30.29511317.152100
2.65-2.7614.30.25711288.828100
2.76-2.8814.20.22211626.469100
2.88-3.0314.10.18611347.98100
3.03-3.2213.90.14611455.846100
3.22-3.4713.70.12111675.002100
3.47-3.8213.50.10511606.228100
3.82-4.37130.09311816.731100
4.37-5.5112.30.09111968.26499.9
5.51-50120.085128511.2799.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
ARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.03→47.7 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2231 / WRfactor Rwork: 0.1819 / FOM work R set: 0.8588 / SU B: 7.993 / SU ML: 0.115 / SU R Cruickshank DPI: 0.2001 / SU Rfree: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1167 5.2 %RANDOM
Rwork0.1848 ---
obs0.1869 21471 98.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.62 Å2 / Biso mean: 42.506 Å2 / Biso min: 12.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0 Å2
2---0.04 Å2-0 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 2.03→47.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2634 0 0 140 2774
Biso mean---33.69 -
Num. residues----345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192715
X-RAY DIFFRACTIONr_bond_other_d0.0060.022589
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.9613691
X-RAY DIFFRACTIONr_angle_other_deg1.2435966
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1255353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.16524.274117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28915455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2531516
X-RAY DIFFRACTIONr_chiral_restr0.0970.2421
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0213098
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02598
X-RAY DIFFRACTIONr_mcbond_it2.1982.4941388
X-RAY DIFFRACTIONr_mcbond_other2.1982.4911387
X-RAY DIFFRACTIONr_mcangle_it3.1953.7181734
Refine LS restraints NCS

Ens-ID: 1 / Number: 9275 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.027→2.079 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 71 -
Rwork0.217 1357 -
all-1428 -
obs--86.44 %
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)
11.01810.35480.340.72670.11920.90140.0082-0.07510.14290.0747-0.05570.0525-0.0296-0.01490.04750.02480.00230.00430.038-0.02660.031313.987178.515913.2872
21.7186-1.20570.12474.16591.01632.8177-0.01130.03660.1103-0.87910.0404-0.3293-0.62270.2031-0.0290.3301-0.07930.05680.0719-0.03340.074523.375298.467816.2376
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A136 - 311
2X-RAY DIFFRACTION2B137 - 305

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