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- PDB-2gl2: Crystal structure of the tetra mutant (T66G,R67G,F68G,Y69G) of ba... -

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Basic information

Entry
Database: PDB / ID: 2gl2
TitleCrystal structure of the tetra mutant (T66G,R67G,F68G,Y69G) of bacterial adhesin FadA
Componentsadhesion A
KeywordsCELL ADHESION / antiparallel helix-loop-helix / FadA Gly4 mutant
Function / homologyAdhesion protein FadA / Adhesion protein FadA / Helix Hairpins - #1700 / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / : / Adhesion A
Function and homology information
Biological speciesFusobacterium nucleatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsNithianantham, S. / Xu, M. / Wu, N. / Shoham, M. / Han, Y.W.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Crystallization and preliminary X-ray data of the FadA adhesin from Fusobacterium nucleatum.
Authors: Nithianantham, S. / Xu, M. / Wu, N. / Han, Y.W. / Shoham, M.
History
DepositionApr 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 15, 2023Group: Structure summary / Category: struct / Item: _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: adhesion A
B: adhesion A


Theoretical massNumber of molelcules
Total (without water)26,6592
Polymers26,6592
Non-polymers00
Water4,017223
1
A: adhesion A


Theoretical massNumber of molelcules
Total (without water)13,3291
Polymers13,3291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: adhesion A


Theoretical massNumber of molelcules
Total (without water)13,3291
Polymers13,3291
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.168, 59.168, 188.249
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein adhesion A


Mass: 13329.401 Da / Num. of mol.: 2 / Fragment: residues 19-129 / Mutation: T66G, R67G, F68G, Y69G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Plasmid: pYH1378 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 57117488, UniProt: Q5I6B0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.6
Details: Sodium acetate, beta-octyl glucoside, pH 4.6, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97899 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 1, 2006 / Details: Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 11518 / Num. obs: 11518 / % possible obs: 89.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.062 / Χ2: 1.243 / Net I/σ(I): 16.6
Reflection shellResolution: 2.5→2.59 Å / % possible obs: 49.1 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.56 / Num. unique obs: 632 / Χ2: 1.52 / % possible all: 48.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2AVR

2avr
PDB Unreleased entry


Resolution: 2.5→29.2 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.307 1182 9.2 %RANDOM
Rwork0.232 ---
all0.26 11518 --
obs0.25 11478 89.1 %-
Solvent computationBsol: 34.271 Å2
Displacement parametersBiso mean: 46.112 Å2
Baniso -1Baniso -2Baniso -3
1-8.653 Å2-1.58 Å20 Å2
2--8.653 Å20 Å2
3----17.307 Å2
Refine analyzeLuzzati coordinate error obs: 0.371 Å / Luzzati sigma a obs: 0.214 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 0 223 1912
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg0.889
X-RAY DIFFRACTIONc_mcbond_it1.5091.5
X-RAY DIFFRACTIONc_scbond_it2.422
X-RAY DIFFRACTIONc_mcangle_it2.5852
X-RAY DIFFRACTIONc_scangle_it3.9072.5
LS refinement shellResolution: 2.5→2.54 Å /
RfactorNum. reflection
Rfree0.48 22
Rwork0.406 -
obs-203
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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