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- PDB-1ajo: CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CP... -

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Basic information

Entry
Database: PDB / ID: 1ajo
TitleCIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-127
ComponentsCIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-127
KeywordsHYDROLASE / GLUCANASE / CIRCULAR PERMUTATION
Function / homology
Function and homology information


licheninase activity / licheninase / carbohydrate metabolic process
Similarity search - Function
Beta-glucanase/XTH / 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/XTH / 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 speciesPaenibacillus macerans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsAy, J. / Heinemann, U.
CitationJournal: Proteins / Year: 1998
Title: Crystal structures and properties of de novo circularly permuted 1,3-1,4-beta-glucanases.
Authors: Ay, J. / Hahn, M. / Decanniere, K. / Piotukh, K. / Borriss, R. / Heinemann, U.
History
DepositionMay 7, 1997Processing site: BNL
Revision 1.0May 6, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / 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_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: CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-127
B: CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-127
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9514
Polymers47,8702
Non-polymers802
Water4,396244
1
A: CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-127
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9752
Polymers23,9351
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-127
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,9752
Polymers23,9351
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.950, 46.550, 63.990
Angle α, β, γ (deg.)92.60, 109.28, 116.68
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.72956, -0.15908, 0.66516), (-0.1582, -0.90694, -0.39042), (0.66537, -0.39006, 0.6365)
Vector: -4.0303, 16.604, -30.2478)

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Components

#1: Protein CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-127 / CPA16M-127


Mass: 23935.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus macerans (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P23904, licheninase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBOTH INDEPENDENT MOLECULES OF CPA16M-127 SHOW A CATION BINDING SITE WITH A CALCIUM ION IN ...BOTH INDEPENDENT MOLECULES OF CPA16M-127 SHOW A CATION BINDING SITE WITH A CALCIUM ION IN OCTAHEDRAL COORDINATION.

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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: 2.3 Å3/Da / Density % sol: 46.5 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 9
Details: HANGING DROP METHOD: A SOLUTION OF 18 MG OF PROTEIN PER ML IN 20 MM TRIS/HCL, PH 9.0, 2 MM CA-CHLORIDE, MIXED WITH AN EQUAL VOLUME OF 0.1 M IMIDAZOLE, PH7.5,2 MM CA-CHLORIDE, 10% (BY WEIGHT) ...Details: HANGING DROP METHOD: A SOLUTION OF 18 MG OF PROTEIN PER ML IN 20 MM TRIS/HCL, PH 9.0, 2 MM CA-CHLORIDE, MIXED WITH AN EQUAL VOLUME OF 0.1 M IMIDAZOLE, PH7.5,2 MM CA-CHLORIDE, 10% (BY WEIGHT) PEG 8000 AND 8% (BY VOL.) ETHYLENE GLYCOL., vapor diffusion - hanging drop
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
118 mg/mlprotein1drop
220 mMTris-HCl1drop
32 mM1dropCaCl2
40.1 Mimidazol1reservoir
52 mM1reservoirCaCl2
610 %PEG80001reservoir
78 %ethylene glycol1reservoir

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1995 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.07→29.62 Å / Num. obs: 24275 / % possible obs: 93.5 % / Redundancy: 1.8 % / Biso Wilson estimate: 20.94 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 2.94
Reflection shellResolution: 2.07→2.15 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.196 / Mean I/σ(I) obs: 3.3 / Rsym value: 0.19 / % possible all: 90
Reflection
*PLUS
Num. measured all: 43819
Reflection shell
*PLUS
% possible obs: 90 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AYH

2ayh


Resolution: 2.07→9.99 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2381 9.9 %RANDOM
Rwork0.176 ---
obs-24053 93.5 %-
Displacement parametersBiso mean: 20.8 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 9.99 Å
Refinement stepCycle: LAST / Resolution: 2.07→9.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3376 0 2 244 3622
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.1962.5
X-RAY DIFFRACTIONp_mcangle_it3.0674
X-RAY DIFFRACTIONp_scbond_it2.4032.5
X-RAY DIFFRACTIONp_scangle_it3.4474
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1370.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.97
X-RAY DIFFRACTIONp_staggered_tor16.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 24053 / Rfactor all: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

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