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- PDB-6b7k: GH43 Endo-Arabinanase from Bacillus licheniformis -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6b7k
TitleGH43 Endo-Arabinanase from Bacillus licheniformis
ComponentsEndo-alpha-(1->5)-L-arabinanase
KeywordsHYDROLASE / Arabinanase / Bacillus licheniformis / GH43
Function / homology
Function and homology information


arabinan endo-1,5-alpha-L-arabinanase / arabinan endo-1,5-alpha-L-arabinosidase activity / arabinan catabolic process
Similarity search - Function
Glycoside hydrolase, family 43, endo-1, 5-alpha-L-arabinosidase / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta
Similarity search - Domain/homology
Endo-alpha-(1->5)-L-arabinanase
Similarity search - Component
Biological speciesBacillus licheniformis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsFarro, E.G.S. / Nascimento, A.S.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2014/03768-0 Brazil
Sao Paulo Research Foundation (FAPESP)2014/06565-2 Brazil
CitationJournal: Int. J. Biol. Macromol. / Year: 2018
Title: GH43 endo-arabinanase from Bacillus licheniformis: Structure, activity and unexpected synergistic effect on cellulose enzymatic hydrolysis.
Authors: Farro, E.G.S. / Leite, A.E.T. / Silva, I.A. / Filgueiras, J.G. / de Azevedo, E.R. / Polikarpov, I. / Nascimento, A.S.
History
DepositionOct 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-alpha-(1->5)-L-arabinanase
B: Endo-alpha-(1->5)-L-arabinanase
C: Endo-alpha-(1->5)-L-arabinanase
D: Endo-alpha-(1->5)-L-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,32112
Polymers134,0004
Non-polymers3218
Water1,76598
1
A: Endo-alpha-(1->5)-L-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5803
Polymers33,5001
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Endo-alpha-(1->5)-L-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5803
Polymers33,5001
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Endo-alpha-(1->5)-L-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5803
Polymers33,5001
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Endo-alpha-(1->5)-L-arabinanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5803
Polymers33,5001
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.558, 124.178, 69.231
Angle α, β, γ (deg.)90.00, 91.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Endo-alpha-(1->5)-L-arabinanase


Mass: 33499.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus licheniformis (strain ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46) (bacteria)
Strain: ATCC 14580 / DSM 13 / JCM 2505 / NBRC 12200 / NCIMB 9375 / NRRL NRS-1264 / Gibson 46
Gene: abnA, BL00353
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q65GB9, arabinan endo-1,5-alpha-L-arabinanase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.07 Å3/Da / Density % sol: 40.59 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.05
Details: 0.1 mM HEPES pH 7.05, 10% PEG 4000 (w/v), 5% 2-propanol (v/v)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 20, 2014 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→46.74 Å / Num. obs: 27463 / % possible obs: 77.3 % / Redundancy: 2.1 % / Biso Wilson estimate: 37.388 Å2 / CC1/2: 0.979 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.076 / Rrim(I) all: 0.108 / Net I/σ(I): 7.9
Reflection shellResolution: 2.55→2.66 Å / Redundancy: 2 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3271 / CC1/2: 0.756 / Rpim(I) all: 0.322 / Rrim(I) all: 0.457 / % possible all: 75.6

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Processing

Software
NameVersionClassification
PHENIX1.12rc1_2807refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UV4
Resolution: 2.55→44.518 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.26
RfactorNum. reflection% reflection
Rfree0.2735 1286 4.71 %
Rwork0.2295 --
obs0.2317 27311 76.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.55→44.518 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9085 0 8 98 9191
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039381
X-RAY DIFFRACTIONf_angle_d0.57712809
X-RAY DIFFRACTIONf_dihedral_angle_d8.4725289
X-RAY DIFFRACTIONf_chiral_restr0.0431304
X-RAY DIFFRACTIONf_plane_restr0.0031648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.65210.41081730.33683087X-RAY DIFFRACTION93
2.6521-2.77280.4115840.31542037X-RAY DIFFRACTION94
2.7728-2.91890.32291710.28823704X-RAY DIFFRACTION98
2.9189-3.10180.3431830.30393694X-RAY DIFFRACTION98
3.1018-3.34120.29781970.27413658X-RAY DIFFRACTION98
3.3412-3.67730.3392340.2661809X-RAY DIFFRACTION91
3.6773-4.20910.3034680.22571542X-RAY DIFFRACTION90
4.2091-5.30160.21091980.16693743X-RAY DIFFRACTION99
5.3016-44.5250.21671780.18193751X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.3617-0.7271-4.52092.75351.2636.3166-0.1807-0.2566-0.76980.4574-0.50110.55210.695-0.76840.57280.4298-0.0537-0.00360.4482-0.07720.4343-12.0474-7.801177.3613
22.79280.69830.9192.0227-0.53743.3403-0.0262-0.42650.3950.02140.24140.4128-0.8172-0.3994-0.31060.42030.04390.05780.444-0.10730.4302-4.2227-1.507174.7811
35.11732.4297-4.91372.8567-0.82278.08110.3194-0.16461.014-0.09390.48710.4264-0.6039-0.1511-0.79720.32360.1293-0.08890.3878-0.04720.4324-8.16230.629773.1554
43.8329-0.31520.05693.0316-0.80542.6216-0.05540.447-0.0121-0.56710.2395-0.09630.36840.4397-0.22090.46-0.00510.09140.2975-0.02320.41944.1428-6.272163.4761
54.4041-0.04980.93282.8304-0.58682.6646-0.0950.2830.0059-0.41620.0779-0.49480.23440.2921-0.00650.275-0.00560.08430.2861-0.01080.29247.3377-9.891367.5942
61.3030.10080.62072.21840.03910.2496-0.47020.1739-0.6477-0.7390.5857-0.3683-0.18510.2269-0.13420.2966-0.00680.10140.3612-0.02730.47412.2682-17.55369.6737
73.85871.01290.74983.94340.14556.16070.2469-0.0547-0.191-0.1134-0.0437-0.4690.5337-0.1947-0.160.3894-0.05730.01580.32680.07810.4552.179-23.474277.6458
83.18380.031-2.88385.9886-3.49714.6548-0.2919-1.13310.0373-0.26860.14220.1414-0.75872.19910.21480.4362-0.1207-0.04070.6195-0.13370.844-15.8616-22.301668.8043
91.4295-1.77050.50863.19630.09082.76290.1673-0.4759-0.5160.0089-0.05730.11110.0791-0.0348-0.12070.2926-0.03240.00930.45290.09380.475-1.8441-22.757181.0144
100.11920.43860.41821.9791.53551.3958-0.1364-0.7101-0.34220.1027-0.05060.1673-0.3304-0.55260.10710.2379-0.01710.03080.66060.08040.4751-9.8593-16.265882.6903
112.5399-0.9055-1.79331.60170.55822.3676-0.0421-0.537-0.18160.02340.04550.36020.32950.15480.00980.3410.0249-0.02960.3496-0.06810.5051-21.9056-18.841355.2995
121.7709-1.45570.73721.8097-0.71272.68860.13260.19270.26930.0883-0.28950.0005-0.43530.23440.14310.3206-0.0711-0.0230.3445-0.04020.3326-19.4544-6.923448.1853
131.32221.53651.69815.2101-0.18513.48720.01940.4791-0.0068-0.32070.15630.8013-0.43130.1674-0.20730.60960.04880.05130.41490.11440.3237-22.4941-4.803840.4003
140.78022.1290.30398.78632.94272.9663-0.6009-0.0229-0.148-0.07470.4681-2.7245-0.8031.88420.11850.4883-0.0407-0.07680.5878-0.00710.6792-7.0099-10.828749.5642
151.83260.08320.13424.11560.1381.9896-0.03110.36280.4489-0.9645-0.05930.4512-0.18160.00780.0670.56510.0779-0.03970.40290.05840.3189-26.3889-11.330332.9295
163.5357-0.106-0.21921.130.96361.79770.05790.29440.0272-0.32530.12660.256-0.1556-0.0783-0.20590.46310.0807-0.08330.45670.04760.3065-33.4954-22.247538.057
171.55351.71370.71891.7639-0.21945.02670.0857-0.0981-0.3431-0.0984-0.09270.2036-0.4071-0.4736-0.01730.3650.04470.00060.45060.01010.6088-38.8925-22.879343.5057
181.36632.0364-0.07753.78571.90795.8793-0.46670.63520.3146-0.02980.02070.51390.47840.24250.27210.30220.02320.01530.338-0.06410.5763-23.5595-24.472745.0183
193.2321.1794-1.19743.47641.425.7033-0.28090.11440.27140.43580.57431.17720.95620.0457-0.15260.36580.05290.07810.35770.15280.4361-33.1946-16.45857.2551
204.2566-1.83140.48395.0717-0.43841.9356-0.05310.423-0.5953-0.35480.46130.70740.04460.2642-0.57730.2175-0.06470.00130.5012-0.0830.5083-30.2409-33.090643.5425
214.2217-2.4540.38043.3175-0.04714.95610.1124-0.14150.52030.2615-0.1659-0.13390.0202-0.0880.05220.2888-0.06750.02790.36680.0380.3386-14.5409-43.667955.6097
221.6533-0.8286-1.39863.2456-0.94911.96590.01350.1901-0.5686-0.1417-0.08330.50640.4046-0.10880.06310.4296-0.07-0.05840.4214-0.03790.4256-15.7228-55.486342.3152
231.18811.42360.92822.3328-0.11932.7930.28440.1942-0.1327-0.58930.010.21530.09570.1373-0.23550.5767-0.0250.0480.2545-0.01820.2364-16.0202-53.81442.9637
246.8052-0.5053-0.09091.94361.39031.9133-0.31730.14520.5123-0.1490.3471-0.38910.31160.28380.02230.45160.0407-0.07680.37560.04160.3781-9.5822-54.745234.4142
254.2541-0.99790.06293.8141-0.18963.2526-0.0950.0958-0.2551-0.78110.04380.03360.0106-0.20450.01570.55390.0185-0.01540.3944-0.01590.2635-9.7095-44.574131.2825
261.79542.47420.33875.8248-0.36813.3131-0.2940.6967-0.0617-0.90330.26470.63770.0099-0.15920.00910.4431-0.01040.00640.6112-0.10720.3771-14.2425-47.505727.1643
272.8982-0.23340.25623.04131.05193.4244-0.1210.04350.0623-0.4830.2376-0.4038-0.17480.4872-0.11790.38710.00120.10450.325-0.04220.41920.0933-38.105537.3241
281.773-0.4944-1.09613.0865-0.11973.2313-0.11990.09250.0818-0.00740.08570.39290.12180.3110.04060.3489-0.0172-0.02030.31120.01180.4236-1.3784-37.004146.4281
290.90251.1305-0.12496.0131-0.43575.93420.54470.47020.0710.83550.190.06610.26340.9405-0.70660.25680.0346-0.09160.3903-0.03990.5243-1.4878-43.854257.8774
306.4522-0.89772.70049.76270.65883.7164-0.0073-0.28140.9212-0.27550.1255-0.833-0.03320.25460.05870.36530.01580.04020.3773-0.04450.4372-5.2217-27.607645.0874
314.49312.25050.31011.65530.51333.17060.0844-0.7428-0.27930.6236-0.4761-1.1735-0.38270.6430.3020.4535-0.0849-0.08880.40120.11890.6073-25.9792-53.889978.9178
322.00971.2479-0.49412.3671-2.42548.86530.0122-0.1972-0.2121-0.2488-0.3906-0.79830.86391.01470.40160.36010.03710.02440.39320.15710.6942-29.4372-55.973870.5667
333.28110.49411.27952.6599-0.16784.21360.05260.03680.0043-0.5403-0.0312-0.44320.635-0.2313-0.02380.3698-0.01170.09350.27390.00410.4679-31.978-55.596864.7738
343.40871.1617-1.1823.8871-0.64632.85760.04390.0875-0.4288-0.26640.2410.47760.0481-0.554-0.22750.22860.03170.00180.33080.01940.4729-41.4264-54.229566.7332
351.6661.04190.82712.75090.56362.2879-0.1186-0.0590.4445-0.37360.10120.4122-0.2043-0.35950.01130.32340.0286-0.04040.3480.05830.5115-43.84-40.450172.5395
368.93421.14240.36576.1837-0.32574.21-1.39590.24390.6672-0.44590.79091.0587-0.56770.09560.10560.5426-0.0245-0.14920.39030.1070.5392-22.7111-36.733669.407
377.03032.83820.57632.5314-0.54142.0699-0.1958-0.29481.31930.05220.12930.76570.0402-0.25420.0250.3795-0.0075-0.07420.51190.07720.6309-43.6081-34.706580.8115
381.7206-1.0273-0.83671.41130.3132.42480.4111-0.72180.4199-0.2985-0.0526-0.22950.00310.069-0.31110.247-0.0337-0.07810.464-0.06670.6331-30.4849-33.452678.9147
392.1465-1.45821.27152.1136-2.22496.70330.6686-0.6765-0.1505-0.50350.0768-0.15520.71870.4265-0.70920.4320.0150.05930.4374-0.01390.5406-33.4145-46.954782.5707
401.92540.7192-1.28031.2079-1.24711.45970.0644-0.55810.05620.2507-0.0789-0.1370.02220.15110.05590.4666-0.0727-0.06230.575-0.03080.4211-26.1029-42.498182.4522
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:16)
2X-RAY DIFFRACTION2(chain A and resid 17:34)
3X-RAY DIFFRACTION3(chain A and resid 35:54)
4X-RAY DIFFRACTION4(chain A and resid 55:82)
5X-RAY DIFFRACTION5(chain A and resid 83:143)
6X-RAY DIFFRACTION6(chain A and resid 144:170)
7X-RAY DIFFRACTION7(chain A and resid 171:202)
8X-RAY DIFFRACTION8(chain A and resid 203:209)
9X-RAY DIFFRACTION9(chain A and resid 210:262)
10X-RAY DIFFRACTION10(chain A and resid 263:291)
11X-RAY DIFFRACTION11(chain B and resid 2:23)
12X-RAY DIFFRACTION12(chain B and resid 24:82)
13X-RAY DIFFRACTION13(chain B and resid 83:104)
14X-RAY DIFFRACTION14(chain B and resid 105:110)
15X-RAY DIFFRACTION15(chain B and resid 111:187)
16X-RAY DIFFRACTION16(chain B and resid 188:225)
17X-RAY DIFFRACTION17(chain B and resid 226:252)
18X-RAY DIFFRACTION18(chain B and resid 253:261)
19X-RAY DIFFRACTION19(chain B and resid 262:278)
20X-RAY DIFFRACTION20(chain B and resid 279:291)
21X-RAY DIFFRACTION21(chain C and resid 2:49)
22X-RAY DIFFRACTION22(chain C and resid 50:88)
23X-RAY DIFFRACTION23(chain C and resid 89:111)
24X-RAY DIFFRACTION24(chain C and resid 112:133)
25X-RAY DIFFRACTION25(chain C and resid 134:158)
26X-RAY DIFFRACTION26(chain C and resid 159:171)
27X-RAY DIFFRACTION27(chain C and resid 172:231)
28X-RAY DIFFRACTION28(chain C and resid 232:261)
29X-RAY DIFFRACTION29(chain C and resid 262:276)
30X-RAY DIFFRACTION30(chain C and resid 277:291)
31X-RAY DIFFRACTION31(chain D and resid 2:22)
32X-RAY DIFFRACTION32(chain D and resid 23:34)
33X-RAY DIFFRACTION33(chain D and resid 35:74)
34X-RAY DIFFRACTION34(chain D and resid 75:123)
35X-RAY DIFFRACTION35(chain D and resid 124:200)
36X-RAY DIFFRACTION36(chain D and resid 201:211)
37X-RAY DIFFRACTION37(chain D and resid 212:224)
38X-RAY DIFFRACTION38(chain D and resid 225:252)
39X-RAY DIFFRACTION39(chain D and resid 253:263)
40X-RAY DIFFRACTION40(chain D and resid 264:291)

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