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- PDB-4ooz: Crystal structure of beta-1,4-D-mannanase from Cryptopygus antarc... -

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Basic information

Entry
Database: PDB / ID: 4ooz
TitleCrystal structure of beta-1,4-D-mannanase from Cryptopygus antarcticus in complex with mannopentaose
ComponentsBeta-1,4-mannanase
KeywordsHYDROLASE / Tim Barrel
Function / homology
Function and homology information


mannan catabolic process / mannan endo-1,4-beta-mannosidase / mannan endo-1,4-beta-mannosidase activity / oligosaccharide binding / polysaccharide binding / extracellular region
Similarity search - Function
Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
beta-D-mannopyranose / Mannan endo-1,4-beta-mannosidase
Similarity search - Component
Biological speciesCryptopygus antarcticus (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKim, M.-K. / An, Y.J. / Jeong, C.-S. / Cha, S.-S.
CitationJournal: Proteins / Year: 2014
Title: Structure-based investigation into the functional roles of the extended loop and substrate-recognition sites in an endo-beta-1,4-d-mannanase from the Antarctic springtail, Cryptopygus antarcticus.
Authors: Kim, M.K. / An, Y.J. / Song, J.M. / Jeong, C.S. / Kang, M.H. / Kwon, K.K. / Lee, Y.H. / Cha, S.S.
History
DepositionFeb 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-1,4-mannanase
B: Beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,7418
Polymers85,3902
Non-polymers3,3516
Water1,33374
1
A: Beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3714
Polymers42,6951
Non-polymers1,6753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-1,4-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3714
Polymers42,6951
Non-polymers1,6753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.023, 82.453, 164.324
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A20 - 383
2010B20 - 383

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Components

#1: Protein Beta-1,4-mannanase


Mass: 42695.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptopygus antarcticus (arthropod) / Production host: Escherichia coli (E. coli)
References: UniProt: B4XC07, mannan endo-1,4-beta-mannosidase
#2: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a1122h-1b_1-5]/1-1-1-1/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D- ...beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 828.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,5,4/[a1122h-1b_1-5]/1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-BMA / beta-D-mannopyranose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 2.94 Å3/Da / Density % sol: 58.11 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 8.5
Details: 0.1 M Tris HCl pH 8.5, 25%(w/v) polyethylene glycol (PEG) 3350, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 41340 / % possible obs: 96.7 %
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 1.7 / % possible all: 77.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.1 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.901 / SU ML: 0.38 / σ(F): 1.47 / Phase error: 30.63 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2713 1503 4.85 %
Rwork0.2351 --
obs0.2368 30999 97.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.926 Å2
Baniso -1Baniso -2Baniso -3
1-3.39 Å2-0 Å20 Å2
2--4.43 Å2-0 Å2
3----7.82 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5676 0 226 74 5976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056067
X-RAY DIFFRACTIONf_angle_d0.9618251
X-RAY DIFFRACTIONf_dihedral_angle_d13.8332227
X-RAY DIFFRACTIONf_chiral_restr0.039909
X-RAY DIFFRACTIONf_plane_restr0.0041038
Refine LS restraints NCS

Ens-ID: 1 / Number: 21122 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.15 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.68390.4231330.38392598X-RAY DIFFRACTION96
2.6839-2.77970.36571320.35262605X-RAY DIFFRACTION96
2.7797-2.89090.37741310.33412589X-RAY DIFFRACTION97
2.8909-3.02240.33821330.31412625X-RAY DIFFRACTION97
3.0224-3.18150.31341360.30542646X-RAY DIFFRACTION97
3.1815-3.38060.28221360.27192658X-RAY DIFFRACTION98
3.3806-3.64120.28221370.23012680X-RAY DIFFRACTION98
3.6412-4.00670.24621370.19852705X-RAY DIFFRACTION98
4.0067-4.58460.22521390.17772732X-RAY DIFFRACTION99
4.5846-5.76870.20111400.18112764X-RAY DIFFRACTION99
5.7687-29.10180.23351490.18662894X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -20.9807 Å / Origin y: -7.0614 Å / Origin z: -13.8409 Å
111213212223313233
T0.3346 Å2-0.0731 Å2-0.064 Å2-0.4191 Å20.0037 Å2--0.4312 Å2
L0.8504 °2-0.0955 °2-0.6556 °2-1.0671 °2-0.4272 °2--3.6151 °2
S-0.0208 Å °0.0153 Å °0.0641 Å °-0.0629 Å °-0.0214 Å °-0.1169 Å °-0.1813 Å °0.2418 Å °0.0227 Å °
Refinement TLS groupSelection details: all

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