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- PDB-3at7: Crystal structure of bacterial cell-surface alginate-binding prot... -

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Basic information

Entry
Database: PDB / ID: 3at7
TitleCrystal structure of bacterial cell-surface alginate-binding protein Algp7
ComponentsAlginate-binding flagellin
KeywordsSTRUCTURAL PROTEIN / two up-and-down four-helical bundles / alginate binding / alginate
Function / homology
Function and homology information


cell envelope / metal ion binding
Similarity search - Function
EfeO/Algp7, imelysin-like domain / : / : / M75 peptidase, HXXE motif / Imelysin-like domain / Imelysin-like domain superfamily / Imelysin / A middle domain of Talin 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Alginate-binding protein
Similarity search - Component
Biological speciesSphingomonas (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMaruyama, Y. / Ochiai, A. / Mikami, B. / Hashimoto, W. / Murata, K.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Crystal structure of bacterial cell-surface alginate-binding protein with an M75 peptidase motif.
Authors: Maruyama, Y. / Ochiai, A. / Mikami, B. / Hashimoto, W. / Murata, K.
History
DepositionDec 27, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 31, 2013Group: Database references
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate-binding flagellin
B: Alginate-binding flagellin


Theoretical massNumber of molelcules
Total (without water)63,4022
Polymers63,4022
Non-polymers00
Water4,810267
1
A: Alginate-binding flagellin


Theoretical massNumber of molelcules
Total (without water)31,7011
Polymers31,7011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Alginate-binding flagellin


Theoretical massNumber of molelcules
Total (without water)31,7011
Polymers31,7011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.886, 97.734, 103.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

#1: Protein Alginate-binding flagellin


Mass: 31701.088 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingomonas (bacteria) / Strain: A1 / Gene: p7 / Plasmid: pET44a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q25C86
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.12 Å3/Da / Density % sol: 41.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.1
Details: 10% PEG 8000, 0.2M NaCl, 0.1M Sodium Citrate pH4.1, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 23, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 32186 / % possible obs: 99.9 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 34.5
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.305 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.529 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23605 1629 5.1 %RANDOM
Rwork0.19699 ---
obs0.19899 30484 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.663 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20 Å2
2---0.81 Å20 Å2
3---1.62 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3952 0 0 267 4219
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0224057
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9431.9755473
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1895509
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.8723.744195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.03615735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7241535
X-RAY DIFFRACTIONr_chiral_restr0.0680.2609
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213069
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3361.52509
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.64924018
X-RAY DIFFRACTIONr_scbond_it0.90931548
X-RAY DIFFRACTIONr_scangle_it1.6364.51450
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 136 -
Rwork0.213 2172 -
obs--99.53 %

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