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

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Basic information

Entry
Database: PDB / ID: 1ajk
TitleCIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE CPA16M-84
ComponentsCIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE
KeywordsHYDROLASE / GLUCANASE / CIRCULAR PERMUTATION
Function / homology
Function and homology information


licheninase / licheninase activity / 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
PHOSPHATE ION / Beta-glucanase
Similarity search - Component
Biological speciesPaenibacillus macerans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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 6, 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_asym_id / _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_asym_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_asym_id / _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_asym_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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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
B: CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5227
Polymers47,8702
Non-polymers6525
Water5,459303
1
A: CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3094
Polymers23,9351
Non-polymers3733
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,2143
Polymers23,9351
Non-polymers2782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.450, 65.820, 69.610
Angle α, β, γ (deg.)90.00, 106.87, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.82105, -0.03541, -0.56976), (0.04072, -0.99916, 0.00343), (-0.5694, -0.02038, 0.8218)
Vector: 10.39901, 63.0936, 39.80625)

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Components

#1: Protein CIRCULARLY PERMUTED (1-3,1-4)-BETA-D-GLUCAN 4-GLUCANOHYDROLASE / CPA16M-84


Mass: 23935.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus macerans (bacteria) / Cell line: DH5ALPHA / Plasmid: PTZ19R / Cell line (production host): DH5ALPHA / 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: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsBOTH INDEPENDENT MOLECULES OF CPA16M-84 SHOW A CATION BINDING SITE WITH A CALCIUM ION IN OCTAHEDRAL ...BOTH INDEPENDENT MOLECULES OF CPA16M-84 SHOW A CATION BINDING SITE WITH A CALCIUM ION IN OCTAHEDRAL COORDINATION AND A HEPES BUFFER MOLECULE IN THE ACTIVE SITE. A PHOSPHATE MOLECULE IS BOUND BETWEEN LYS 56 AND ARG 66 OF TWO SYMMETRY-RELATED MOLECULES.

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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 %
Description: ONE LOW- AND ONE HIGH-RESOLUTION DATA SET WERE COLLECTED FROM ONE CRYSTAL.
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: SITTING DROP METHOD: A SOLUTION OF 12 MG OF PROTEIN PER ML IN 10 MM HEPES, PH 7.0, 2 MM CA-CHLORIDE, MIXED WITH AN EQUAL VOLUME OF 50 MM K-PHOSPHATE, PH 7.0 AND 20% (BY WEIGHT) PEG 8000, ...Details: SITTING DROP METHOD: A SOLUTION OF 12 MG OF PROTEIN PER ML IN 10 MM HEPES, PH 7.0, 2 MM CA-CHLORIDE, MIXED WITH AN EQUAL VOLUME OF 50 MM K-PHOSPHATE, PH 7.0 AND 20% (BY WEIGHT) PEG 8000, vapor diffusion - sitting drop
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
25 mMHEPES1drop
31 mM1dropCaCl2
425 mMpotassium phosphate1drop
510 %PEG80001drop
650 mMpotassium phosphate1reservoir
720 %PEG80001reservoir

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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: Apr 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.76→33.33 Å / Num. obs: 38698 / % possible obs: 98.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 19.34 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 5.8
Reflection shellResolution: 1.76→1.83 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.164 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.16 / % possible all: 94.4
Reflection
*PLUS
Num. measured all: 132154
Reflection shell
*PLUS
% possible obs: 94.4 %

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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: 1.8→33.33 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1786 5.08 %RANDOM
Rwork0.168 ---
obs-35910 98.3 %-
Displacement parametersBiso mean: 20.83 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 33.3 Å
Refinement stepCycle: LAST / Resolution: 1.8→33.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3284 0 38 303 3625
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0350.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.2072.5
X-RAY DIFFRACTIONp_mcangle_it3.1314
X-RAY DIFFRACTIONp_scbond_it2.842.5
X-RAY DIFFRACTIONp_scangle_it4.0994
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1730.15
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_tor15.915
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: 35910 / Rfactor all: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS

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