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- PDB-4b9p: Biomass sensoring module from putative Rsgi2 protein of Clostridi... -

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Basic information

Entry
Database: PDB / ID: 4b9p
TitleBiomass sensoring module from putative Rsgi2 protein of Clostridium thermocellum resemble family 3 carbohydrate-binding module of cellulosome
ComponentsTYPE 3A CELLULOSE-BINDING DOMAIN PROTEIN
KeywordsCARBOHYDRATE-BINDING PROTEIN / CELLULOSE / RSGI-LIKE PROTEINS / BIOMASS SENSING SYSTEM
Function / homology
Function and homology information


cellulose binding / carbohydrate metabolic process / metal ion binding / plasma membrane
Similarity search - Function
: / Anti-sigma factor RsgI-like central domain / Anti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / Endoglucanase-like / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. ...: / Anti-sigma factor RsgI-like central domain / Anti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / Endoglucanase-like / Cellulose binding domain / Carbohydrate-binding module 3 / Cellulose binding domain / CBM3 (carbohydrate binding type-3) domain profile. / Carbohydrate-binding module 3 superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Anti-sigma-I factor RsgI2
Similarity search - Component
Biological speciesCLOSTRIDIUM THERMOCELLUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.182 Å
AuthorsYaniv, O. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Fine-Structural Variance of Family 3 Carbohydrate-Binding Modules as Extracellular Biomass-Sensing Components of Clostridium Thermocellum Anti-Sigma(I) Factors.
Authors: Yaniv, O. / Fichman, G. / Borovok, I. / Shoham, Y. / Bayer, E.A. / Lamed, R. / Shimon, L.J.W. / Frolow, F.
History
DepositionSep 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references / Source and taxonomy
Revision 1.2Feb 26, 2014Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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

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Assembly

Deposited unit
A: TYPE 3A CELLULOSE-BINDING DOMAIN PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1615
Polymers18,9251
Non-polymers2364
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.736, 62.289, 79.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TYPE 3A CELLULOSE-BINDING DOMAIN PROTEIN


Mass: 18924.992 Da / Num. of mol.: 1
Fragment: FAMILY 3B CARBOHYDRATE BINDING MODULE, RESIDUES 506-671
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM THERMOCELLUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: A3DC27
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 2.1 Å3/Da / Density % sol: 41.4 % / Description: NONE
Crystal growpH: 6.5
Details: 0.005 M ZNSO4, 0.1 M MES PH 6.5, 23% (V/V) PEG MME 550

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2011 / Details: MIRRORS
RadiationMonochromator: LIQUID NITROGEN COOLED CHANNEL-CUT SILICON MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.18→50 Å / Num. obs: 52558 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Biso Wilson estimate: 18.67 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16
Reflection shellResolution: 1.18→1.2 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4B97

4b97


Resolution: 1.182→48.978 Å / SU ML: 0.09 / σ(F): 1.36 / Phase error: 18.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1499 2242 5.2 %
Rwork0.124 --
obs0.1254 43413 82.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 0.1049 Å2 / ksol: 1.4007 e/Å3
Displacement parametersBiso mean: 24.686 Å2
Baniso -1Baniso -2Baniso -3
1-1.1234 Å20.5213 Å2-0.1525 Å2
2---0.0591 Å2-0.3717 Å2
3----0.8377 Å2
Refinement stepCycle: LAST / Resolution: 1.182→48.978 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1336 0 4 214 1554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0131451
X-RAY DIFFRACTIONf_angle_d1.5171995
X-RAY DIFFRACTIONf_dihedral_angle_d13.761532
X-RAY DIFFRACTIONf_chiral_restr0.106223
X-RAY DIFFRACTIONf_plane_restr0.008258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1817-1.20730.2037130.1664232X-RAY DIFFRACTION8
1.2073-1.23540.2291390.1736669X-RAY DIFFRACTION22
1.2354-1.26630.2191810.16761265X-RAY DIFFRACTION42
1.2663-1.30060.24511010.16131955X-RAY DIFFRACTION64
1.3006-1.33880.19181470.15762843X-RAY DIFFRACTION92
1.3388-1.38210.18911590.14982982X-RAY DIFFRACTION97
1.3821-1.43150.18911690.14293045X-RAY DIFFRACTION99
1.4315-1.48880.16831690.12893063X-RAY DIFFRACTION100
1.4888-1.55650.1571460.11613108X-RAY DIFFRACTION100
1.5565-1.63860.17251730.10323069X-RAY DIFFRACTION100
1.6386-1.74130.14191700.09893096X-RAY DIFFRACTION100
1.7413-1.87570.14331640.09923098X-RAY DIFFRACTION100
1.8757-2.06450.12791720.09733117X-RAY DIFFRACTION100
2.0645-2.36320.13331640.10633138X-RAY DIFFRACTION100
2.3632-2.97740.16591810.13313172X-RAY DIFFRACTION100
2.9774-49.02040.14311940.13593319X-RAY DIFFRACTION100

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