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- PDB-5kle: Structure of CBM_E1, a novel carbohydrate-binding module found by... -

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Basic information

Entry
Database: PDB / ID: 5kle
TitleStructure of CBM_E1, a novel carbohydrate-binding module found by sugar cane soil metagenome, complexed with cellopentaose
ComponentsCarbohydrate binding module E1
KeywordsSUGAR BINDING PROTEIN / Carbohydrate-binding protein / metagenomics / cellulose / biofuels
Function / homologybeta-cellopentaose / Carbohydrate binding module E1
Function and homology information
Biological speciesuncultured bacterium (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsLiberato, M.V. / Campos, B.M. / Zeri, A.C.M. / Squina, F.M.
Funding support Brazil, 3items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/04105-4 Brazil
Sao Paulo Research Foundation (FAPESP)2013/06336-0 Brazil
Sao Paulo Research Foundation (FAPESP)2008/58037-9 Brazil
CitationJournal: J.Biol.Chem. / Year: 2016
Title: A Novel Carbohydrate-binding Module from Sugar Cane Soil Metagenome Featuring Unique Structural and Carbohydrate Affinity Properties.
Authors: Campos, B.M. / Liberato, M.V. / Alvarez, T.M. / Zanphorlin, L.M. / Ematsu, G.C. / Barud, H. / Polikarpov, I. / Ruller, R. / Gilbert, H.J. / Zeri, A.C. / Squina, F.M.
History
DepositionJun 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Database references
Revision 1.2Jan 17, 2018Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_special_symmetry.auth_asym_id / _pdbx_struct_special_symmetry.auth_comp_id / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbohydrate binding module E1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,8412
Polymers10,0121
Non-polymers8291
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.812, 88.812, 88.812
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-3-

BGC

21A-712-

HOH

31A-764-

HOH

41A-771-

HOH

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Components

#1: Protein Carbohydrate binding module E1


Mass: 10011.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: A0A0R5P8X1
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-cellopentaose


Type: oligosaccharide, Oligosaccharide / Class: Metabolism / Mass: 828.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-cellopentaose
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a2122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.96 Å3/Da / Density % sol: 58.42 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 4 M sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 0.96 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96 Å / Relative weight: 1
ReflectionResolution: 1.5→44.41 Å / Num. obs: 18747 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.034 / Rrim(I) all: 0.085 / Net I/σ(I): 17.9 / Num. measured all: 114680 / Scaling rejects: 1
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique allCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.535.60.84447498520.7040.3860.932.290.7
8.22-44.415.30.0227051320.9990.0110.0255898

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.08 Å36.26 Å
Translation5.08 Å36.26 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
Aimless0.5.21data scaling
PHASER2.6.1phasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KLF

5klf


Resolution: 1.5→36.257 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1829 925 4.93 %
Rwork0.155 17821 -
obs0.1564 18746 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.61 Å2 / Biso mean: 17.2661 Å2 / Biso min: 7.46 Å2
Refinement stepCycle: final / Resolution: 1.5→36.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms694 0 56 182 932
Biso mean--20.68 31.15 -
Num. residues----95
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.022792
X-RAY DIFFRACTIONf_angle_d1.7161087
X-RAY DIFFRACTIONf_chiral_restr0.108109
X-RAY DIFFRACTIONf_plane_restr0.007129
X-RAY DIFFRACTIONf_dihedral_angle_d14.218251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4999-1.5790.21851550.20562428258397
1.579-1.67790.22251080.179325672675100
1.6779-1.80750.1752990.16625322631100
1.8075-1.98930.18851550.156725522707100
1.9893-2.27720.17571160.146125612677100
2.2772-2.86880.18691330.158925582691100
2.8688-36.26790.17241590.141726232782100
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)
10.2634-0.02420.39440.1137-0.06750.6143-0.2042-0.02160.06590.03070.12870.0317-0.1489-0.0662-0.05240.1021-0.00040.01580.1089-0.00590.082820.3794-21.4849-2.1326
21.3343-0.81960.58291.9976-0.90271.35340.00580.2250.0955-0.0247-0.0580.0243-0.11560.1420.06370.1232-0.016-0.01080.10490.01520.119719.7387-10.0709-16.0807
31.08420.0591-0.10831.9293-2.09553.8603-0.02580.1304-0.0995-0.02850.0012-0.04160.05790.2775-0.00830.1155-0.0029-0.0180.1143-0.00770.118316.2049-18.2396-15.9705
41.2828-1.06040.45883.3137-0.76851.3602-0.1123-0.05830.25910.13810.0028-0.1051-0.2090.06760.07560.1405-0.0126-0.03640.0883-0.00360.13518.5002-7.5334-9.2398
51.2612-0.24110.96071.98931.19493.063-0.18480.0460.2072-0.01620.0897-0.0705-0.36930.04060.07480.17970.0122-0.01630.0831-0.00180.133610.2784-3.0638-12.5398
61.0659-0.13020.88660.81750.58922.64090.0203-0.1518-0.03250.06380.0425-0.01460.0513-0.1705-0.02420.1120.0015-0.00490.10840.00950.09468.1616-13.8623-10.8087
71.1408-0.4761-0.30182.0527-0.54033.0129-0.0348-0.05990.0182-0.03790.0320.0113-0.1932-0.23710.02770.12480.0184-0.01810.10530.00180.11344.1401-9.7101-15.584
81.80320.74171.06612.67780.58412.25280.0505-0.14860.03170.1848-0.0594-0.1809-0.1574-0.23850.01330.12530.0199-0.00810.1081-0.00630.086713.2176-10.27-6.5493
90.7317-0.02120.59864.53631.52951.7153-0.0530.05730.1045-0.13640.0033-0.1342-0.2280.0570.04510.1125-0.0074-0.01120.08260.00980.075411.6576-10.6426-17.8613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 333 through 342 )A333 - 342
2X-RAY DIFFRACTION2chain 'A' and (resid 343 through 352 )A343 - 352
3X-RAY DIFFRACTION3chain 'A' and (resid 353 through 359 )A353 - 359
4X-RAY DIFFRACTION4chain 'A' and (resid 360 through 365 )A360 - 365
5X-RAY DIFFRACTION5chain 'A' and (resid 366 through 374 )A366 - 374
6X-RAY DIFFRACTION6chain 'A' and (resid 375 through 390 )A375 - 390
7X-RAY DIFFRACTION7chain 'A' and (resid 391 through 401 )A391 - 401
8X-RAY DIFFRACTION8chain 'A' and (resid 402 through 416 )A402 - 416
9X-RAY DIFFRACTION9chain 'A' and (resid 417 through 427 )A417 - 427

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