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- PDB-2xhj: Circular permutation provides an evolutionary link between two fa... -

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Basic information

Entry
Database: PDB / ID: 2xhj
TitleCircular permutation provides an evolutionary link between two families of calcium-dependent carbohydrate binding modules. SeMet form of vCBM60.
ComponentsCALCIUM-DEPENDENT CARBOHYDRATE BINDING MODULE
KeywordsSUGAR BINDING PROTEIN / LECTIN / XYLAN / CELLULOSE / GALACTAN / BETA GLUCAN
Function / homologyLipoxygenase-1 - #40 / Lipoxygenase-1 / Sandwich / Mainly Beta
Function and homology information
Biological speciesCELLVIBRIO JAPONICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.73 Å
AuthorsMontanier, C. / Flint, J.E. / Bolam, D.N. / Xie, H. / Liu, Z. / Rogowski, A. / Weiner, D. / Ratnaparkhe, S. / Nurizzo, D. / Roberts, S.M. ...Montanier, C. / Flint, J.E. / Bolam, D.N. / Xie, H. / Liu, Z. / Rogowski, A. / Weiner, D. / Ratnaparkhe, S. / Nurizzo, D. / Roberts, S.M. / Turkenburg, J.P. / Davies, G.J. / Gilbert, H.J.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Circular Permutation Provides an Evolutionary Link between Two Families of Calcium-Dependent Carbohydrate Binding Modules
Authors: Montanier, C. / Flint, J.E. / Bolam, D.N. / Xie, H. / Liu, Z. / Rogowski, A. / Weiner, D. / Ratnaparkhe, S. / Nurizzo, D. / Roberts, S.M. / Turkenburg, J.P. / Davies, G.J. / Gilbert, H.J.
History
DepositionJun 16, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 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 / pdbx_struct_conn_angle / struct_conn / struct_site
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CALCIUM-DEPENDENT CARBOHYDRATE BINDING MODULE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9722
Polymers12,9321
Non-polymers401
Water1,874104
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.805, 45.805, 102.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein CALCIUM-DEPENDENT CARBOHYDRATE BINDING MODULE


Mass: 12931.747 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: SELENOMETHIONINE FORM OF THE PROTEIN USED FOR PHASING
Source: (gene. exp.) CELLVIBRIO JAPONICUS (bacteria) / Strain: NCIMB 10462 / Description: NCIMB CULTURE COLLECTION / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 (NOVAGEN)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsCURRENTLY NO UNIPROT REFERENCE EXISTS FOR ENTRY. ISOLATED GENE IS GENBANK REF: FN908918 AND THE ...CURRENTLY NO UNIPROT REFERENCE EXISTS FOR ENTRY. ISOLATED GENE IS GENBANK REF: FN908918 AND THE EXPRESSED PROTEIN SEQUENCE IS GENBANK REF: CBM95521.1 TITLE: CARBOHYDRATE BINDING MODULE [UNCULTURED BACTERIUM] FIRST DBREF CARD REFERS TO THE PROTEIN SEQUENCE WITH A MUTATED N-TERMINAL RESIDUE (SER REPLACES MET) SECOND DBREF CARD REFERS TO AN C-TERMINAL EXPRESSION TAG

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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: 2.05 Å3/Da / Density % sol: 40 %
Description: THIS IS THE SEMET CRYSTAL FORM USED TO SOLVE THE NATIVE.
Crystal growTemperature: 293 K / pH: 6
Details: CRYSTALS WERE GROWN AT 4 DEGREES C OR 20 DEGREES C IN 2.1M NA MALATE PH 5.5-6.0 AT A 1:1 OR 3:2 RATIO OF PROTEIN TO MOTHER LIQUOR

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.75→34.1 Å / Num. obs: 11819 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 13.5 % / Biso Wilson estimate: 18.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 34.8
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 12.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXCDphasing
SHELXEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.73→41.81 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.277 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21701 570 4.9 %RANDOM
Rwork0.12569 ---
obs0.12989 11142 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.124 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2--0.18 Å20 Å2
3----0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.73→41.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms906 0 1 104 1011
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021938
X-RAY DIFFRACTIONr_bond_other_d0.0010.02568
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.8681285
X-RAY DIFFRACTIONr_angle_other_deg0.90731387
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5445124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1962550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.04115137
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.509155
X-RAY DIFFRACTIONr_chiral_restr0.0930.2145
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021106
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02192
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_it6.2612591
X-RAY DIFFRACTIONr_mcbond_other2.3312253
X-RAY DIFFRACTIONr_mcangle_it7.5993954
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.0792347
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it10.433328
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.90531506
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.726→1.771 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 29 -
Rwork0.133 524 -
obs--88.48 %

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