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- PDB-1mve: Crystal structure of a natural circularly-permutated jellyroll pr... -

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Basic information

Entry
Database: PDB / ID: 1mve
TitleCrystal structure of a natural circularly-permutated jellyroll protein: 1,3-1,4-beta-D-glucanase from Fibrobacter succinogenes
ComponentsTruncated 1,3-1,4-beta-D-glucanase
KeywordsHYDROLASE / circular-permutated jellyroll protein
Function / homology
Function and homology information


licheninase activity / licheninase / carbohydrate metabolic process
Similarity search - Function
Beta-glucanase / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / : / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls ...Beta-glucanase / Glycoside hydrolase, family 16, active site / Glycosyl hydrolases family 16 active sites. / : / Glycosyl hydrolases family 16 / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesFibrobacter succinogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsTsai, L.-C. / Shyur, L.-F. / Lee, S.-H. / Lin, S.-S. / Yuan, H.S.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal Structure of a Natural Circularly Permuted Jellyroll Protein: 1,3-1,4-beta-D-Glucanase from Fibrobacter succinogenes.
Authors: Tsai, L.C. / Shyur, L.F. / Lee, S.H. / Lin, S.S. / Yuan, H.S.
History
DepositionSep 25, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _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: Truncated 1,3-1,4-beta-D-glucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4052
Polymers27,3651
Non-polymers401
Water5,044280
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.850, 73.350, 73.710
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 Truncated 1,3-1,4-beta-D-glucanase / ENDO-BETA-1 / 3-1 / 4 GLUCANASE / MIXED LINKAGE BETA-GLUCANASE / LICHENASE


Mass: 27365.361 Da / Num. of mol.: 1 / Fragment: Residues 1-243
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Fibrobacter succinogenes (bacteria) / Plasmid: pET26b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3) / References: UniProt: P17989, licheninase
#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.: 280 / 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: 1.88 Å3/Da / Density % sol: 33.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, sodium acetate, Tris-HCL, calcium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
32 mM1reservoirCaCl2
40.1 M1reservoirCH3COONa
50.05 MTris-HCl1reservoirpH9.0
630 %(w/v)PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 0.9795, 0.9793, 0.9600
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 19, 2001
RadiationMonochromator: Si 111 + Ge 220 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
20.97931
30.961
ReflectionResolution: 1.7→32.93 Å / Num. obs: 24553 / % possible obs: 99.5 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 14 Å2 / Rsym value: 0.067 / Net I/σ(I): 22.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 3 / Num. unique all: 24553 / Rsym value: 0.308 / % possible all: 92.8
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 98 % / Num. measured all: 108344 / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
Highest resolution: 1.7 Å / % possible obs: 92.8 % / Rmerge(I) obs: 0.308

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→32.93 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 161500.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2343 9.8 %RANDOM
Rwork0.192 ---
obs0.21 23837 95.1 %-
all-24553 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.2604 Å2 / ksol: 0.35602 e/Å3
Displacement parametersBiso mean: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.85 Å20 Å20 Å2
2---0.45 Å20 Å2
3----1.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.7→32.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1916 0 1 280 2197
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
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_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it2.022
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 348 9.9 %
Rwork0.236 3175 -
obs--86.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 40 Å / Rfactor Rfree: 0.238
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.63
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74
LS refinement shell
*PLUS
Lowest resolution: 1.76 Å

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