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- PDB-4b96: Family 3b carbohydrate-binding module from the biomass sensoring ... -

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Basic information

Entry
Database: PDB / ID: 4b96
TitleFamily 3b carbohydrate-binding module from the biomass sensoring system of Clostridium clariflavum
ComponentsCELLULOSE BINDING DOMAIN-CONTAINING PROTEIN
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE BINDING PROTEIN SYSTEM / CELLULOSE
Function / homology
Function and homology information


cellulose binding / membrane => GO:0016020 / carbohydrate metabolic process / plasma membrane
Similarity search - Function
Anti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / Endoglucanase-like / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / CBM2/CBM3, carbohydrate-binding domain superfamily ...Anti-sigma factor RsgI, N-terminal / Anti-sigma factor N-terminus / RsgI N-terminal anti-sigma domain profile. / Endoglucanase-like / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Cellulose binding domain-containing protein
Similarity search - Component
Biological speciesCLOSTRIDIUM CLARIFLAVUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.911 Å
AuthorsYaniv, O. / Reddy, Y.H.K. / Yoffe, H. / Shimon, L.J.W. / Bayer, E.A. / Lamed, R. / Frolow, F.
CitationJournal: To be Published
Title: Structure of Cbm3B from the Biomass Sensoring System of Clostridium Clarifalvum
Authors: Yaniv, O. / Reddy, Y.H.K. / Bayer, E.A. / Lamed, R. / Frolow, F.
History
DepositionSep 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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.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.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.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_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: CELLULOSE BINDING DOMAIN-CONTAINING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1655
Polymers18,0191
Non-polymers1464
Water3,063170
1
A: CELLULOSE BINDING DOMAIN-CONTAINING PROTEIN
hetero molecules

A: CELLULOSE BINDING DOMAIN-CONTAINING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,33110
Polymers36,0382
Non-polymers2938
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area2730 Å2
ΔGint-100.3 kcal/mol
Surface area14330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.212, 135.212, 54.323
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-2068-

HOH

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Components

#1: Protein CELLULOSE BINDING DOMAIN-CONTAINING PROTEIN


Mass: 18018.988 Da / Num. of mol.: 1 / Fragment: RESIDUES 333-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM CLARIFLAVUM (bacteria)
Description: GERMAN COLLECTION OF MICROORGANISMS (DSM) 19732
Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): RIL / References: UniProt: G8LST1
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.11 Å3/Da / Density % sol: 41.7 % / Description: NONE
Crystal growpH: 4.6 / Details: 2.0 M NACL, 0.1 M NA ACETATE PH 4.6

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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: May 17, 2012 / 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: 1.91→50 Å / Num. obs: 23184 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 4.68 % / Biso Wilson estimate: 22.39 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 11.8
Reflection shellResolution: 1.91→1.94 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 1.7 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CLOSTRIDIUM THERMOCELLUM 0404 CBM3B

Resolution: 1.911→49.278 Å / SU ML: 0.13 / σ(F): 1.36 / Phase error: 17.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1889 1051 5.1 %
Rwork0.1528 --
obs0.1546 20626 47.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 378 Å2 / ksol: 0.69 e/Å3
Displacement parametersBiso mean: 30.277 Å2
Refinement stepCycle: LAST / Resolution: 1.911→49.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 4 170 1453
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0191361
X-RAY DIFFRACTIONf_angle_d1.6671851
X-RAY DIFFRACTIONf_dihedral_angle_d13.853489
X-RAY DIFFRACTIONf_chiral_restr0.149183
X-RAY DIFFRACTIONf_plane_restr0.008239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9115-1.99850.225700.1991189X-RAY DIFFRACTION23
1.9985-2.10380.22091060.18312142X-RAY DIFFRACTION42
2.1038-2.23560.21451390.16982496X-RAY DIFFRACTION49
2.2356-2.40830.19511620.17382613X-RAY DIFFRACTION51
2.4083-2.65060.21871240.16442718X-RAY DIFFRACTION53
2.6506-3.03410.22231660.15852726X-RAY DIFFRACTION54
3.0341-3.82240.17851550.13282755X-RAY DIFFRACTION54
3.8224-49.29480.1511290.14222936X-RAY DIFFRACTION57
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.5243-3.46520.38814.7663-0.18772.2954-0.2103-0.2462-0.75490.0650.11680.4694-0.0293-0.53530.04450.1625-0.0238-0.00410.243-0.02410.197465.001953.9795.2808
29.45731.66492.29446.1856-1.10587.2309-0.0027-0.1824-0.90890.02120.1313-0.53470.21720.004-0.07620.18240.0291-0.0160.2351-0.0350.265388.84649.69558.3476
32.71240.15840.12931.7430.16541.8137-0.02680.2320.058-0.2120.04780.0576-0.0746-0.03240.01180.1424-0.001-0.00590.12250.00540.117577.575658.5048-0.0595
42.91760.1378-0.43610.9428-2.03564.7743-0.0490.48890.1783-0.8130.2442-0.235-0.79520.459-0.25760.26290.03450.03740.230.0330.174781.930464.3831-4.0539
53.08290.50090.57182.4548-0.14421.97280.00710.07730.2563-0.11890.00750.0358-0.1682-0.07750.08780.1529-0.02060.01110.1452-0.00450.140578.97961.62492.3274
63.47614.6617-4.05929.2247-6.79135.4396-0.19180.1842-0.0812-0.53590.3475-0.26280.5376-0.15680.06170.1934-0.0616-0.00750.2761-0.02270.27596.665458.83935.837
73.5808-0.33450.38451.73830.29873.32630.0345-0.1620.00910.0485-0.0314-0.0740.15250.04210.00350.0952-0.03540.01070.11290.01540.095875.563156.440810.7585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1 THROUGH 9 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 10 THROUGH 19 )
3X-RAY DIFFRACTION3CHAIN A AND (RESID 20 THROUGH 64 )
4X-RAY DIFFRACTION4CHAIN A AND (RESID 65 THROUGH 75 )
5X-RAY DIFFRACTION5CHAIN A AND (RESID 76 THROUGH 109 )
6X-RAY DIFFRACTION6CHAIN A AND (RESID 110 THROUGH 116 )
7X-RAY DIFFRACTION7CHAIN A AND (RESID 117 THROUGH 151 )

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