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- PDB-3wsu: Crystal structure of beta-mannanase from Streptomyces thermolilacinus -

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Basic information

Entry
Database: PDB / ID: 3wsu
TitleCrystal structure of beta-mannanase from Streptomyces thermolilacinus
ComponentsBeta-mannanase
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
Biological speciesStreptomyces thermolilacinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 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
DepositionMar 26, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Oct 14, 2015Group: Other
Revision 1.3Oct 28, 2015Group: Database references
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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.ptnr2_auth_asym_id / _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_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_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: Beta-mannanase
B: Beta-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,43512
Polymers74,7912
Non-polymers64510
Water14,376798
1
A: Beta-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6265
Polymers37,3951
Non-polymers2304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-mannanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8107
Polymers37,3951
Non-polymers4146
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.864, 100.846, 105.244
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Beta-mannanase


Mass: 37395.438 Da / Num. of mol.: 2 / Fragment: UNP residues 36-349
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces thermolilacinus (bacteria)
Strain: NBRC 14274 / Gene: beta-mannanase / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL / References: UniProt: F5HR99
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 798 / 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: 2.34 Å3/Da / Density % sol: 47.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.1M sodium malonate, 0.1M HEPES, 0.5%(v/v) Jeffamine(R) ED-2001, pH 7.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 11, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→48.846 Å / Num. obs: 90737 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 5.06 % / Biso Wilson estimate: 7.95 Å2 / Rmerge(I) obs: 0.18 / Χ2: 0.937 / Net I/σ(I): 9.96
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.6-1.70.6220.8122.257244914889147920.91399.3
1.7-1.810.7070.6193.096895513959138750.69799.4
1.81-1.960.8450.4144.726473213071129460.46599
1.96-2.150.9250.2657.335991212056118690.29898.4
2.15-2.40.9570.18810.035446810937106670.21197.5
2.4-2.770.9770.14112.8848361970993770.15896.6
2.77-3.390.9920.08719.4340936824378340.09795
3.39-4.780.9980.04731.431753647260140.05292.9
4.78-500.9990.04232.917570375833630.04689.5

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_1426refinement
PDB_EXTRACT3.14data extraction
BSSdata collection
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1bqc

1bqc


Resolution: 1.6→45.473 Å / FOM work R set: 0.891 / SU ML: 0.16 / Phase error: 18.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1938 1810 1.99 %
Rwork0.1601 --
obs0.1608 90733 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 54.1 Å2 / Biso mean: 12.05 Å2 / Biso min: 3.59 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.473 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4571 0 40 798 5409
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084766
X-RAY DIFFRACTIONf_angle_d1.1886505
X-RAY DIFFRACTIONf_chiral_restr0.082692
X-RAY DIFFRACTIONf_plane_restr0.005861
X-RAY DIFFRACTIONf_dihedral_angle_d13.4871657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5995-1.64280.29531370.23916837697499
1.6428-1.69110.27271440.227169287072100
1.6911-1.74570.22981390.21386901704099
1.7457-1.80810.25281350.20216883701899
1.8081-1.88050.22771430.18446947709099
1.8805-1.96610.21441490.176851700099
1.9661-2.06980.1921360.15886891702799
2.0698-2.19940.18321400.14756852699298
2.1994-2.36920.19261340.14816835696998
2.3692-2.60760.17521390.14746801694097
2.6076-2.98490.18451430.14696777692096
2.9849-3.76040.14561380.13366707684594
3.7604-45.49170.16311330.13356713684691
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)
10.6160.0557-0.26390.5939-0.01930.6167-0.02450.0791-0.0616-0.09090.0166-0.01910.047-0.0020.00850.0559-0.0040.00650.0545-0.01370.056445.398265.7576-14.4261
21.66830.02190.7721.9747-0.06481.1740.00030.06460.067-0.02050.0054-0.0064-0.08780.0341-0.00270.0488-0.00150.01930.0518-0.00470.035645.392581.9187-8.7677
31.81110.11510.36981.08880.56260.54970.0795-0.1672-0.02460.0569-0.0386-0.0501-0.01350.059-0.02560.054-0.0057-0.00450.06030.01020.038550.729970.92922.799
42.67680.9018-0.14091.94870.21112.8086-0.00460.0050.14910.0394-0.00950.304-0.0963-0.1713-0.02910.0531-0.00220.00390.05680.00110.071811.525835.0651.2079
52.1931.22960.25861.82870.25630.74740.01910.15510.002-0.07230.0301-0.1122-0.01260.0468-0.03790.03740.00570.00030.05130.00030.057432.206436.7967-5.1867
62.49341.37851.45511.41510.60791.1663-0.09510.14060.011-0.09540.0803-0.0157-0.06940.14940.02090.04710.00110.00110.04590.01070.047431.666548.4807-2.2161
70.68350.02470.13770.8412-0.01080.763-0.0238-0.05940.02110.07950.0131-0.011-0.021-0.00570.01190.04870.0027-0.00420.044-0.00240.05725.015642.558411.2404
83.4766-1.9492-1.90236.59411.07642.5741-0.1443-0.3201-0.19530.30870.0503-0.01580.25220.00970.06480.0986-0.01590.00470.08990.02520.057520.655724.549516.6064
90.5551-0.2583-0.26581.4245-0.18381.27980.0196-0.15870.02630.12020.0193-0.05770.0150.1638-0.00460.0674-0.006-0.00520.0815-0.0060.046432.046527.236411.0744
101.87910.3614-1.14752.0212-0.59291.4758-0.00590.0896-0.0863-0.01630.02880.11060.1226-0.027-0.03310.0645-0.0073-0.00190.05360.00030.058823.53523.04685.7434
111.6194-0.3953-0.16221.0848-0.14540.5748-0.01810.0895-0.1149-0.06120.0143-0.04290.05960.0475-0.00320.0645-0.00150.00110.0489-0.01420.044332.193327.3482-4.191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 53 through 251 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 252 through 302 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 303 through 352 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 52 through 71 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 72 through 103 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 104 through 126 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 127 through 251 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 252 through 265 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 266 through 285 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 286 through 302 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 303 through 349 )B0

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