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- PDB-4zgv: The Crystal Structure of the Ferredoxin Receptor FusA from Pectob... -

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Basic information

Entry
Database: PDB / ID: 4zgv
TitleThe Crystal Structure of the Ferredoxin Receptor FusA from Pectobacterium atrosepticum SCRI1043
ComponentsFerredoxin receptor
KeywordsTRANSPORT PROTEIN / Beta-barrel / TonB-dependent receptor / Iron-transporter / Outer membrane
Function / homologyTonB-dependent receptor, plug domain superfamily / TonB-dependent receptor, plug domain / TonB-dependent receptor-like, beta-barrel domain superfamily / TonB-dependent Receptor Plug Domain / Plug domain-containing protein
Function and homology information
Biological speciesPectobacterium atrosepticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.2 Å
AuthorsGrinter, R. / Josts, I. / Roszak, A.W. / Cogdell, R.J. / Walker, D.
CitationJournal: Nat Commun / Year: 2016
Title: Structure of the bacterial plant-ferredoxin receptor FusA.
Authors: Grinter, R. / Josts, I. / Mosbahi, K. / Roszak, A.W. / Cogdell, R.J. / Bonvin, A.M. / Milner, J.J. / Kelly, S.M. / Byron, O. / Smith, B.O. / Walker, D.
History
DepositionApr 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 31, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferredoxin receptor
B: Ferredoxin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,2018
Polymers195,5732
Non-polymers1,6286
Water362
1
A: Ferredoxin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,1226
Polymers97,7871
Non-polymers1,3365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferredoxin receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0792
Polymers97,7871
Non-polymers2921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)137.274, 79.886, 137.905
Angle α, β, γ (deg.)90.00, 90.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Ferredoxin receptor


Mass: 97786.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium atrosepticum (bacteria) / Strain: SCRI 1043 / ATCC BAA-672 / Gene: ECA0878 / Plasmid: pETFA1043 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6D8U4
#2: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#3: Sugar
ChemComp-BOG / octyl beta-D-glucopyranoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.87 Å3/Da / Density % sol: 68.23 %
Description: Long thin needles, up to 1 mM by 50 uM. Very fragile, bent easily, difficult to handle
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 11-14 % PVP, 14 % PEG 2000 MME, 0.1 Tris, 0.05 M MgCl2 pH 7.5, with a FusA concentration of 15 mg.ml-1 in 50 mM Tris, 200 mM NaCl, 0.8-1 % (v/v) beta-OG, 0.4 % LDAO pH 7.9, at 289 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9765 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2014
RadiationMonochromator: Silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9765 Å / Relative weight: 1
ReflectionResolution: 3.2→48.95 Å / Num. obs: 49734 / % possible obs: 100 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.305 / Net I/σ(I): 7
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.73 / Mean I/σ(I) obs: 1.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 3.2→48.95 Å / Cor.coef. Fo:Fc: 0.889 / Cor.coef. Fo:Fc free: 0.881 / SU B: 58.57 / SU ML: 0.408 / Cross valid method: THROUGHOUT / ESU R Free: 0.464 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2511 5.1 %RANDOM
Rwork0.21834 ---
obs0.221 47173 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.354 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20 Å2-0.13 Å2
2--4.16 Å2-0 Å2
3----2.13 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12900 0 112 2 13014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213378
X-RAY DIFFRACTIONr_bond_other_d0.0070.0211872
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.93318164
X-RAY DIFFRACTIONr_angle_other_deg1.041327331
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.69651616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.55624.414691
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.156152052
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9051570
X-RAY DIFFRACTIONr_chiral_restr0.0910.21870
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02115568
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023378
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0095.4396470
X-RAY DIFFRACTIONr_mcbond_other3.0065.4396469
X-RAY DIFFRACTIONr_mcangle_it4.9378.1638084
X-RAY DIFFRACTIONr_mcangle_other4.9378.1638085
X-RAY DIFFRACTIONr_scbond_it3.3945.8526908
X-RAY DIFFRACTIONr_scbond_other3.3885.8526908
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6368.64410081
X-RAY DIFFRACTIONr_long_range_B_refined8.32144.27514428
X-RAY DIFFRACTIONr_long_range_B_other8.32344.28214429
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 159 -
Rwork0.374 3453 -
obs--99.92 %
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)
11.2278-0.04080.05180.55940.06831.06320.04510.19520.2854-0.1202-0.1704-0.0318-0.12970.07430.12530.04070.0260.00550.27450.02450.093537.575318.708748.896
21.07840.1327-0.70220.94360.29431.40880.14840.3230.0831-0.1319-0.16690.2319-0.1743-0.38450.01850.04920.0478-0.02680.3682-0.01840.0915-28.957418.82521.311
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A59 - 867
2X-RAY DIFFRACTION2B59 - 867

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