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- PDB-4y7e: Crystal structure of beta-mannanase from Streptomyces thermolilac... -

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Basic information

Entry
Database: PDB / ID: 4y7e
TitleCrystal structure of beta-mannanase from Streptomyces thermolilacinus with mannohexaose
ComponentsEndoglucanase
KeywordsHYDROLASE / Mannanase / glycoside hydrolase family 5 / actinomycete
Function / homology
Function and homology information


cellulase / cellulase activity / polysaccharide binding / cellulose catabolic process / metal ion binding
Similarity search - Function
Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Fibronectin type III domain / Fibronectin type 3 domain ...Cellulose binding domain / Carbohydrate-binding type-2 domain / CBM2 (Carbohydrate-binding type-2) domain profile. / CBD_II / CBM2, carbohydrate-binding domain superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / Fibronectin type III domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Alpha Beta
Similarity search - Domain/homology
beta-D-mannopyranose / Endoglucanase
Similarity search - Component
Biological speciesStreptomyces thermolilacinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsKumagai, Y. / Yamashita, K. / Okuyama, M. / Hatanaka, T. / Yao, M. / Kimura, A.
CitationJournal: Febs J. / Year: 2015
Title: The loop structure of Actinomycete glycoside hydrolase family 5 mannanases governs substrate recognition
Authors: Kumagai, Y. / Yamashita, K. / Tagami, T. / Uraji, M. / Wan, K. / Okuyama, M. / Yao, M. / Kimura, A. / Hatanaka, T.
History
DepositionFeb 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 23, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Feb 5, 2020Group: Data collection / Derived calculations / Category: chem_comp / diffrn_source / pdbx_struct_oper_list
Item: _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_struct_conn_angle / struct_asym / 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_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endoglucanase
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,43823
Polymers74,6752
Non-polymers3,76421
Water14,322795
1
A: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,01613
Polymers37,3371
Non-polymers2,67812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,42310
Polymers37,3371
Non-polymers1,0859
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2920 Å2
ΔGint-11 kcal/mol
Surface area21440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.709, 100.706, 104.737
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Endoglucanase


Mass: 37337.402 Da / Num. of mol.: 2 / Fragment: UNP residues 36-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces thermolilacinus (bacteria)
Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: F5HR99, cellulase

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Sugars , 3 types, 9 molecules

#2: 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-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 1153.001 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,7,6/[a1122h-1b_1-5]/1-1-1-1-1-1-1/a4-b1_b4-c1_c4-d1_d4-e1_e4-f1_f4-g1WURCSPDB2Glycan 1.1.0
#3: Polysaccharide beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-4)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpb1-4DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a1122h-1b_1-5]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Manp]{[(4+1)][b-D-Manp]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Sugar
ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 7
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

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Non-polymers , 3 types, 807 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 795 / 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: 2.32 Å3/Da / Density % sol: 46.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.1M sodium malonate pH 7.0, 0.1M HEPES pH 7.0, 0.5%(v/v) Jeffamine(R) ED-2001 pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 21, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→48.7 Å / Num. obs: 117826 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 4.56 % / Biso Wilson estimate: 9.9 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.097 / Rrim(I) all: 0.11 / Χ2: 0.905 / Net I/σ(I): 12.29 / Num. measured all: 537026
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.45-1.540.7010.5911.874470719729148020.7175
1.54-1.640.8480.4713.177354818624180220.5496.8
1.64-1.780.9270.3694.728513517339173250.41299.9
1.78-1.940.970.2297.37888215984159700.25699.9
1.94-2.170.9890.13312.27177314489144800.14899.9
2.17-2.510.9940.09116.976375012873128610.10299.9
2.51-3.070.9970.06223.055420510931109170.06999.9
3.07-4.330.9990.03536.6842000855585500.0499.9
4.330.9990.0341.7623026494948990.03399

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Processing

Software
NameVersionClassificationNB
PHENIX1.9_1690refinement
XDSdata reduction
PDB_EXTRACT3.15data extraction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3WSU

3wsu


Resolution: 1.5→46.462 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1727 2172 1.98 %
Rwork0.1458 --
obs0.1464 109429 97.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→46.462 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4577 0 238 795 5610
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0115049
X-RAY DIFFRACTIONf_angle_d1.3986874
X-RAY DIFFRACTIONf_dihedral_angle_d14.0631795
X-RAY DIFFRACTIONf_chiral_restr0.072786
X-RAY DIFFRACTIONf_plane_restr0.007870
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4999-1.53250.26011010.22845410X-RAY DIFFRACTION80
1.5325-1.56820.20491360.20576105X-RAY DIFFRACTION90
1.5682-1.60740.19561250.19046705X-RAY DIFFRACTION99
1.6074-1.65090.21851340.18016759X-RAY DIFFRACTION100
1.6509-1.69950.20561420.17376762X-RAY DIFFRACTION100
1.6995-1.75430.17371390.16476749X-RAY DIFFRACTION100
1.7543-1.8170.21611390.15666823X-RAY DIFFRACTION100
1.817-1.88980.17331350.14596782X-RAY DIFFRACTION100
1.8898-1.97580.18741330.13686832X-RAY DIFFRACTION100
1.9758-2.07990.16061390.13556774X-RAY DIFFRACTION100
2.0799-2.21030.14691370.12866856X-RAY DIFFRACTION100
2.2103-2.38090.17661470.13186834X-RAY DIFFRACTION100
2.3809-2.62050.1691360.13916861X-RAY DIFFRACTION100
2.6205-2.99960.17641440.14036886X-RAY DIFFRACTION100
2.9996-3.77890.13651370.13156952X-RAY DIFFRACTION100
3.7789-46.48420.1631480.1377167X-RAY DIFFRACTION99
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)
12.43210.0554-0.63344.439-0.56693.5635-0.01370.0431-0.0178-0.14140.02210.17150.0874-0.153-0.0010.05440.00020.00030.062-0.0050.082330.587167.7199-6.7179
22.3468-0.5727-1.67961.08861.01012.664-0.037-0.0937-0.10650.01410.0354-0.11020.13660.12710.00550.0511-0.00380.0020.050.0020.07851.601563.071-2.3126
33.11420.6525-3.16770.6591-0.95343.382-0.1376-0.0289-0.2355-0.0955-0.0263-0.08010.18490.08930.16610.0830.00420.01290.0635-0.00970.107451.247855.0299-11.7751
40.56510.0508-0.21650.58480.03710.8289-0.03170.0973-0.0551-0.12650.0165-0.03130.0477-0.0140.02020.0904-0.00440.01320.089-0.01690.084445.723565.0441-19.3477
51.29841.00740.14162.09730.04080.7794-0.01620.12270.0434-0.14430.04020.0692-0.0305-0.0752-0.01310.08130.01030.01340.0911-0.00540.0741.134676.1973-18.2965
61.6285-0.4680.60330.9338-0.30930.6820.0350.01260.059-0.0118-0.0195-0.0368-0.04090.0394-0.01570.0694-0.00740.01320.0744-0.01150.073449.778977.9606-5.856
72.96432.19580.52982.57090.45910.33540.1238-0.19950.01750.2265-0.12880.03830.0053-0.01350.00320.0914-0.00030.00330.0827-0.00690.076843.113571.85014.9695
83.06081.012-0.35973.43220.54485.971-0.02960.00020.04030.0538-0.00220.3253-0.1332-0.26520.00680.0445-0.00220.0060.0588-0.00110.108511.303835.03831.1571
91.80041.39160.80212.9140.9821.1192-0.00180.1207-0.0165-0.10230.0539-0.1192-0.05180.0575-0.04750.05250.0097-0.0020.0709-0.00190.082532.035436.7671-5.2446
102.71381.68111.59441.91661.04281.3546-0.09690.13090.0017-0.10590.10380.0126-0.09690.093-0.01870.06460.00180.00650.06530.00480.079931.497948.364-2.2336
110.4320.28640.44531.11880.58141.8921-0.00510.02950.03290.0380.0011-0.0226-0.03550.04150.02160.0516-0.00570.00370.06310.00620.093628.889647.41596.1782
120.6499-0.02720.28180.80250.06160.7442-0.0211-0.06840.01920.08960.01250.0249-0.0089-0.01850.00990.06810.0013-0.00050.06440.00050.079623.140940.165513.4778
131.624-0.9945-0.68941.30640.02511.66980.0123-0.15460.0480.1290.0268-0.01110.06440.0753-0.02820.0887-0.0217-0.0090.0684-0.00740.08727.459825.835813.168
142.46330.501-0.87985.0224-0.81721.2895-0.04060.0063-0.1079-0.04150.03070.08460.1301-0.00110.00580.0723-0.0087-0.00860.0674-0.00610.053223.328423.06085.7096
151.8348-0.49650.00761.1464-0.13890.24770.0230.1034-0.1441-0.0633-0.0051-0.01380.05280.025-0.02240.0743-0.00210.00080.0726-0.01540.075932.206427.2618-4.1517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 51 through 71 )
2X-RAY DIFFRACTION2chain 'A' and (resid 72 through 103 )
3X-RAY DIFFRACTION3chain 'A' and (resid 104 through 126 )
4X-RAY DIFFRACTION4chain 'A' and (resid 127 through 221 )
5X-RAY DIFFRACTION5chain 'A' and (resid 222 through 251 )
6X-RAY DIFFRACTION6chain 'A' and (resid 252 through 325 )
7X-RAY DIFFRACTION7chain 'A' and (resid 326 through 352 )
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 71 )
9X-RAY DIFFRACTION9chain 'B' and (resid 72 through 103 )
10X-RAY DIFFRACTION10chain 'B' and (resid 104 through 126 )
11X-RAY DIFFRACTION11chain 'B' and (resid 127 through 164 )
12X-RAY DIFFRACTION12chain 'B' and (resid 165 through 251 )
13X-RAY DIFFRACTION13chain 'B' and (resid 252 through 285 )
14X-RAY DIFFRACTION14chain 'B' and (resid 286 through 302 )
15X-RAY DIFFRACTION15chain 'B' and (resid 303 through 349 )

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