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- PDB-3etx: Crystal structure of bacterial adhesin FadA L14A mutant -

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Basic information

Entry
Database: PDB / ID: 3etx
TitleCrystal structure of bacterial adhesin FadA L14A mutant
ComponentsAdhesin A
KeywordsCELL ADHESION / antiparallel helix-loop-helix / FadA L14A mutant / Cell adhesin
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: 3 Å
AuthorsNithianantham, S. / Xu, M. / Wu, N. / Shoham, M. / Han, Y.W.
Citation
Journal: J.Biol.Chem. / Year: 2009
Title: Crystal Structure of FadA Adhesin from Fusobacterium nucleatum Reveals a Novel Oligomerization Motif, the Leucine Chain.
Authors: Nithianantham, S. / Xu, M. / Yamada, M. / Ikegami, A. / Shoham, M. / Han, Y.W.
#1: Journal: 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
DepositionOct 8, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionDec 2, 2008ID: 2BC6
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 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 1.3Oct 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 1.4Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adhesin A
B: Adhesin A
C: Adhesin A


Theoretical massNumber of molelcules
Total (without water)40,8833
Polymers40,8833
Non-polymers00
Water1,838102
1
A: Adhesin A


Theoretical massNumber of molelcules
Total (without water)13,6281
Polymers13,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adhesin A


Theoretical massNumber of molelcules
Total (without water)13,6281
Polymers13,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Adhesin A


Theoretical massNumber of molelcules
Total (without water)13,6281
Polymers13,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.317, 104.805, 59.854
Angle α, β, γ (deg.)90.000, 105.100, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain: (Details: chain A,B,C, using restrain)

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Components

#1: Protein Adhesin A


Mass: 13627.759 Da / Num. of mol.: 3 / Mutation: L14A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fusobacterium nucleatum (bacteria) / Gene: fadA / Plasmid: pET21(b) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5I6B0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 4.39 Å3/Da / Density % sol: 72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M Imidazole pH 7.5, and 0.5M sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å
DetectorType: SBC-2 / Detector: CCD / Date: Mar 25, 2005 / Details: 3 x 3 mosaic
RadiationMonochromator: Double crystal (Si-111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 3→38.8 Å / Num. all: 14001 / Num. obs: 13703 / % possible obs: 97.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 62.6 Å2 / Rmerge(I) obs: 0.097 / Χ2: 0.898
Reflection shellResolution: 3→3.11 Å / Redundancy: 3 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 2.4 / Num. unique all: 1284 / Χ2: 0.839 / % possible all: 93.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ETW

3etw


Resolution: 3→38.8 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.778 / Isotropic thermal model: Restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1389 9.8 %Random
Rwork0.238 ---
all0.298 14001 --
obs0.24 13651 96 %-
Solvent computationBsol: 50.81 Å2
Displacement parametersBiso max: 118.33 Å2 / Biso mean: 68.09 Å2 / Biso min: 23.02 Å2
Baniso -1Baniso -2Baniso -3
1--7.131 Å20 Å2-21.691 Å2
2---0.897 Å20 Å2
3---8.028 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.61 Å
Refinement stepCycle: LAST / Resolution: 3→38.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 0 102 2657
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.097
X-RAY DIFFRACTIONc_mcbond_it1.7711.5
X-RAY DIFFRACTIONc_scbond_it3.0422
X-RAY DIFFRACTIONc_mcangle_it3.0262
X-RAY DIFFRACTIONc_scangle_it5.1372.5
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDRmsTypeWeight
11BX-RAY DIFFRACTION0.116restrain100
11CX-RAY DIFFRACTION0.108restrain100
LS refinement shellResolution: 3→3.04 Å /
RfactorNum. reflection
Rfree0.449 19
Rwork0.361 -
obs-208
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top

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