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- PDB-2bh0: Crystal structure of a SeMet derivative of EXPA from Bacillus sub... -

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Basic information

Entry
Database: PDB / ID: 2bh0
TitleCrystal structure of a SeMet derivative of EXPA from Bacillus subtilis at 2.5 angstrom
ComponentsYOAJ
KeywordsCELL ADHESION / EXPANSIN RELATED PROTEIN / BACILLUS SUBTILIS / EXPANSINS
Function / homology
Function and homology information


extracellular region
Similarity search - Function
: / : / Expansin, cellulose-binding-like domain / RlpA-like protein, double-psi beta-barrel domain / Expansin, cellulose-binding-like domain superfamily / Lytic transglycolase / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Immunoglobulin-like ...: / : / Expansin, cellulose-binding-like domain / RlpA-like protein, double-psi beta-barrel domain / Expansin, cellulose-binding-like domain superfamily / Lytic transglycolase / RlpA-like domain / RlpA-like domain superfamily / Barwin-like endoglucanases / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBACILLUS SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsPetrella, S. / Herman, R. / Sauvage, E. / Filee, P. / Joris, B. / Charlier, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2008
Title: Crystal Structure and Activity of Bacillus Subtilis Yoaj (Exlx1), a Bacterial Expansin that Promotes Root Colonization.
Authors: Kerff, F. / Amoroso, A. / Herman, R. / Sauvage, E. / Petrella, S. / Fileee, P. / Charlier, P. / Joris, B. / Tabuchi, A. / Nikolaidis, N. / Cosgrove, D.J.
History
DepositionJan 6, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: YOAJ


Theoretical massNumber of molelcules
Total (without water)23,4711
Polymers23,4711
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)144.035, 144.035, 144.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein YOAJ / EXPA


Mass: 23471.482 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BACILLUS SUBTILIS (bacteria) / Strain: 168 / References: UniProt: O34918
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O
Compound detailsEXPANSINS ARE PLANT CELL WALL PROTEINS FIRST DISCOVERED IN STUDIES OF PLANT CELL ENLARGEMENT. THEY ...EXPANSINS ARE PLANT CELL WALL PROTEINS FIRST DISCOVERED IN STUDIES OF PLANT CELL ENLARGEMENT. THEY HAVE UNIQUE "LOOSENING" EFFECTS ON PLANT CELL WALLS AND ARE THOUGHT TO FUNCTION IN PLANT CELL GROWTH, CELL WALL DISASSEMBLY, CELL SEPARATION, POLLEN TUBE PENETRATION (IN GRASSES, AT LEAST) AND LEAF PRIMORDIUM INITIATION.
Has protein modificationY
Sequence detailsTHE SIGNAL PEPTIDE OF THE PROTEIN USED FOR THE CRYSTALLISATION EXPERIMENTS WAS REMOVED (RESIDUES 1 TO 25).

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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: 5.19 Å3/Da / Density % sol: 76 %
Crystal growDetails: 4M NAFORMATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 6, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→25.46 Å / Num. obs: 17348 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 21.8 % / Biso Wilson estimate: 41.1 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 31.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 21.1 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 5.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→25.46 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2987475.25 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 1584 9.1 %RANDOM
Rwork0.203 ---
obs0.203 17350 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.875 Å2 / ksol: 0.418993 e/Å3
Displacement parametersBiso mean: 33.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.5→25.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1617 0 0 92 1709
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it2.32
X-RAY DIFFRACTIONc_scangle_it3.412.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.361 138 4.8 %
Rwork0.303 2726 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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