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- PDB-4amx: CRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- ... -

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Basic information

Entry
Database: PDB / ID: 4amx
TitleCRYSTAL STRUCTURE OF THE GRACILARIOPSIS LEMANEIFORMIS ALPHA-1,4- GLUCAN LYASE Covalent Intermediate Complex with 5-fluoro-glucosyl- fluoride
ComponentsALPHA-1,4-GLUCAN LYASE ISOZYME 1
KeywordsLYASE / ANHYDROFRUCTOSE PATHWAY / GLYCOSIDE HYDROLASE FAMILY 31 / SECONDARY CARBOHYDRATE BINDING SITE
Function / homology
Function and homology information


exo-(1->4)-alpha-D-glucan lyase / exo-(1,4)-alpha-D-glucan lyase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
glycosyl hydrolase (family 31) / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like ...glycosyl hydrolase (family 31) / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
5-fluoro-beta-D-glucopyranose / Chem-AFR / Alpha-1,4-glucan lyase isozyme 1
Similarity search - Component
Biological speciesGRACILARIOPSIS LEMANEIFORMIS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsRozeboom, H.J. / Yu, S. / Madrid, S. / Kalk, K.H. / Dijkstra, B.W.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal Structure of Alpha-1,4-Glucan Lyase, a Unique Glycoside Hydrolase Family Member with a Novel Catalytic Mechanism.
Authors: Rozeboom, H.J. / Yu, S. / Madrid, S. / Kalk, K.H. / Zhang, R. / Dijkstra, B.W.
History
DepositionMar 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2013Group: Database references
Revision 1.2Sep 25, 2013Group: Database references
Revision 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Jul 29, 2020Group: Advisory / Derived calculations ...Advisory / Derived calculations / Other / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.7Nov 20, 2024Group: Structure summary / Category: 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: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
B: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
C: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
D: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,48413
Polymers464,2494
Non-polymers1,2359
Water16,628923
1
A: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4444
Polymers116,0621
Non-polymers3823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,3523
Polymers116,0621
Non-polymers2902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,2602
Polymers116,0621
Non-polymers1981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ALPHA-1,4-GLUCAN LYASE ISOZYME 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,4264
Polymers116,0621
Non-polymers3643
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.643, 97.008, 135.708
Angle α, β, γ (deg.)80.38, 83.11, 85.22
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 6 / Auth seq-ID: 14 - 1038 / Label seq-ID: 3 - 1027

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

NCS oper:
IDCodeMatrixVector
1given(0.2758, 0.6682, -0.691), (-0.6568, 0.6559, 0.3721), (0.7018, 0.3512, 0.6197)52.17, -36.45, -43.27
2given(0.2765, -0.6605, 0.698), (-0.6579, -0.6596, -0.3635), (0.7005, -0.3587, -0.6169)29.1, -1.906, -55.66
3given(1, 0.00135, 0.000651), (0.001352, -1, -0.001804), (0.000649, 0.001805, -1)-53.97, 2.637, 21.07

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Components

#1: Protein
ALPHA-1,4-GLUCAN LYASE ISOZYME 1


Mass: 116062.156 Da / Num. of mol.: 4 / Fragment: RESIDUES 62-1088
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GRACILARIOPSIS LEMANEIFORMIS (eukaryote)
Production host: OGATAEA POLYMORPHA RB11 (fungus)
References: UniProt: Q9STC1, exo-(1->4)-alpha-D-glucan lyase
#2: Sugar ChemComp-5GF / 5-fluoro-beta-D-glucopyranose / 5-fluoro-beta-D-glucose / 5-fluoro-D-glucose / 5-fluoro-glucose


Type: D-saccharide, beta linking / Mass: 198.146 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C6H11FO6
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Sugar ChemComp-AFR / alpha-D-threo-hexo-2,5-diulo-5,1-pyranosyl fluoride / 2-OXO-1,2,DIDEOXY-5F-D-GLUCOPYRANOSE / alpha-D-threo-hexo-2,5-diulo-5,1-syl fluoride / D-threo-hexo-2,5-diulo-5,1-syl fluoride / threo-hexo-2,5-diulo-5,1-syl fluoride


Type: D-saccharide / Mass: 180.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H9FO5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 923 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer details5-FLUORO-ALPHA-D-GLUCOPYRANOSE (5GF): THE GLUCOSE FORM OF B9D 2-OXO-1,2,DIDEOXY-5F-D-GLUCOPYRANOSE ...5-FLUORO-ALPHA-D-GLUCOPYRANOSE (5GF): THE GLUCOSE FORM OF B9D 2-OXO-1,2,DIDEOXY-5F-D-GLUCOPYRANOSE (AFR): NHF WITH F ATOM AT C5

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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: 2.51 Å3/Da / Density % sol: 51 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 18-21% PEG 8000, 0.1 M SODIUM ACETATE, PH 5.0-5.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9748
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9748 Å / Relative weight: 1
ReflectionResolution: 2.1→47.7 Å / Num. obs: 255868 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.4 / % possible all: 92.3

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2X2H

2x2h


Resolution: 2.1→46.74 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.902 / SU B: 17.242 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.266 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26742 12914 5 %RANDOM
Rwork0.22022 ---
obs0.22263 242819 95.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.721 Å2
Baniso -1Baniso -2Baniso -3
1--2.73 Å20.03 Å2-0.03 Å2
2---0.48 Å22.47 Å2
3---2.38 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32648 0 78 923 33649
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02233620
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.92945735
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.7985.0194108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34824.6261805
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.701155139
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.76515188
X-RAY DIFFRACTIONr_chiral_restr0.0920.24696
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02126840
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4591.520313
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.805232761
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.36313307
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9934.512972
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 8128 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.45
2Bloose positional0.325
3Cloose positional0.335
4Dloose positional0.345
1Aloose thermal4.7810
2Bloose thermal3.6610
3Cloose thermal3.8710
4Dloose thermal3.5510
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 924 -
Rwork0.307 17120 -
obs--91.52 %
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)
12.6973-0.01751.04610.6432-0.61961.00530.0061-0.1347-0.279-0.1315-0.0496-0.13270.0718-0.01650.04340.2581-0.00280.02080.1408-0.0970.174-9.4875-53.7755-1.667
21.24250.33460.60431.1919-0.34540.63610.0592-0.1237-0.14180.0163-0.1242-0.1111-0.0177-0.02960.0650.1767-0.0035-0.01580.1104-0.05560.16053.179-52.577.5448
30.93340.2634-0.28930.8477-0.60770.46180.01620.04330.05960.0039-0.00750.03820.0059-0.0278-0.00870.24180.0074-0.00150.1479-0.12180.1103-1.4582-29.882-7.1847
41.96491.1840.2181.51020.17440.5835-0.05950.18150.0365-0.17670.0972-0.04030.0254-0.0043-0.03770.1860.02690.02130.1698-0.03240.0294.482-32.3185-30.1328
50.68460.2745-0.1840.1648-0.13730.13790.01820.04790.05660.01070.04080.0225-0.01260.0055-0.0590.29630.01420.00320.1525-0.12570.12572.1838-22.6307-8.8338
60.782-0.15980.24340.9148-0.14810.3548-0.0037-0.0090.05350.0553-0.0746-0.1988-0.07250.08230.07830.1712-0.0191-0.00920.104-0.0660.167527.3384-13.21376.2507
71.9904-0.31380.34781.1108-0.38960.50270.1548-0.0109-0.4253-0.293-0.1337-0.20610.26950.1934-0.02110.24470.1105-0.02030.30470.13720.274425.0127-33.53158.0628
81.4496-0.3130.16710.9611-0.32880.62390.0972-0.2323-0.2002-0.005-0.104-0.07550.08580.15220.00680.19090.0131-0.03220.27330.09180.120918.2112-26.128770.8273
90.7008-0.16540.3370.6261-0.37390.62630.0873-0.0345-0.0824-0.1462-0.0760.03140.13860.0439-0.01140.21940.0038-0.02730.16190.00220.0871-3.9147-11.800648.055
101.1168-0.45740.16877.371-2.35962.59390.18460.0439-0.2612-0.4910.05510.0730.49330.0126-0.23970.20620.0217-0.1430.1780.04180.1893-4.6376-28.44443.4249
110.5673-0.10140.37680.7498-0.4760.75550.0708-0.178-0.1683-0.12080.00270.08470.05910.0377-0.07350.2164-0.0126-0.03190.22560.02870.115-0.3437-14.713558.7143
121.3855-0.06670.01570.8666-0.2380.6448-0.0131-0.05360.28890.0426-0.071-0.0969-0.08090.12960.08420.1842-0.0566-0.03860.20490.02460.145112.296413.064859.782
132.71550.0412-0.31511.3233-0.11550.29170.07470.08160.55850.1599-0.0296-0.1417-0.16810.1513-0.04510.203-0.07710.04260.18730.11220.268861.508739.6334-39.9657
140.96980.4722-0.38120.6741-0.36790.52080.00160.12590.08220.0078-0.0216-0.0318-0.05840.06260.020.13460.00980.03040.19420.06680.174547.630221.5736-39.4353
153.99870.0262-1.12094.2456-1.76574.84910.1561-0.21290.20470.39620.0940.4341-0.4281-0.3654-0.25010.19910.04030.14730.07010.04150.223128.891937.0254-22.4588
160.69451.0228-0.7953.9864-0.85211.89720.2048-0.0540.19490.32230.04690.1386-0.21450.0389-0.25170.1312-0.00370.05770.14770.03930.248136.612823.2222-21.0387
170.81320.2655-0.37020.6943-0.2290.45420.00420.1970.04130.00410.003-0.01660.0003-0.0076-0.00720.15950.01190.02820.1950.02330.139138.30115.712-39.2467
181.43170.0168-0.01891.3735-0.24260.9183-0.05920.1424-0.3263-0.07030.0128-0.18890.19380.10610.04640.11390.03590.08510.18910.03170.314250.4656-12.6551-36.8705
190.66140.1687-0.50240.5569-0.50210.65920.0158-0.0090.16240.08450.06470.0174-0.0758-0.0662-0.08050.2030.025-0.00070.124-0.11420.157650.2755.857222.745
201.4898-0.59960.08590.9998-0.60680.47170.05750.105-0.0075-0.05740.00250.150.0617-0.0916-0.060.21350.0048-0.02680.1506-0.10830.12645.061941.858316.4746
210.2673-0.20680.16880.5801-0.13840.29940.0151-0.1275-0.04530.05580.00830.0682-0.0015-0.0307-0.02340.1809-0.0077-0.00480.1648-0.05950.098260.853928.662238.1675
224.7363-2.3886-0.78124.0493-0.31541.0858-0.1016-0.585-0.22670.2210.16990.0628-0.1362-0.0352-0.06830.19990.0286-0.00120.27750.00370.047455.638138.509350.6665
230.7491-0.39180.01510.3623-0.18990.2148-0.0007-0.1186-0.1151-0.01080.07190.1056-0.0057-0.0006-0.07130.2612-0.0206-0.02460.1704-0.10220.139556.359124.914429.7037
240.83770.1121-0.26211.2016-0.33170.33270.0255-0.01460.0271-0.0692-0.0733-0.09890.04860.02650.04780.21390.0167-0.01290.127-0.1020.112381.684416.323814.8596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 88
2X-RAY DIFFRACTION2A89 - 167
3X-RAY DIFFRACTION3A168 - 442
4X-RAY DIFFRACTION4A443 - 555
5X-RAY DIFFRACTION5A556 - 842
6X-RAY DIFFRACTION6A843 - 1038
7X-RAY DIFFRACTION7B14 - 125
8X-RAY DIFFRACTION8B126 - 313
9X-RAY DIFFRACTION9B314 - 480
10X-RAY DIFFRACTION10B481 - 555
11X-RAY DIFFRACTION11B556 - 800
12X-RAY DIFFRACTION12B801 - 1038
13X-RAY DIFFRACTION13C14 - 102
14X-RAY DIFFRACTION14C103 - 468
15X-RAY DIFFRACTION15C469 - 521
16X-RAY DIFFRACTION16C522 - 557
17X-RAY DIFFRACTION17C558 - 828
18X-RAY DIFFRACTION18C829 - 1038
19X-RAY DIFFRACTION19D14 - 125
20X-RAY DIFFRACTION20D126 - 284
21X-RAY DIFFRACTION21D285 - 480
22X-RAY DIFFRACTION22D481 - 556
23X-RAY DIFFRACTION23D557 - 848
24X-RAY DIFFRACTION24D849 - 1038

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