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- PDB-3eu8: Crystal structure of putative glucoamylase (YP_210071.1) from Bac... -

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Basic information

Entry
Database: PDB / ID: 3eu8
TitleCrystal structure of putative glucoamylase (YP_210071.1) from Bacteroides fragilis NCTC 9343 at 2.12 A resolution
Componentsputative glucoamylaseGlucan 1,4-a-glucosidase
KeywordsHYDROLASE / YP_210071.1 / putative glucoamylase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Unknown function
Function / homology
Function and homology information


Protein of unknown function DUF3131 / Protein of unknown function (DUF3131) / Glycoside hydrolase 144 (GH144) / Uncharacterised conserved protein UCP028431 / Glycoamylase-like, conserved domain / Putative glucoamylase / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
: / Conserved hypothetical exported protein
Similarity search - Component
Biological speciesBacteroides fragilis NCTC 9343 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.12 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative glucoamylase (YP_210071.1) from Bacteroides fragilis NCTC 9343 at 2.12 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / 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_conn.ptnr2_label_seq_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: putative glucoamylase
B: putative glucoamylase
C: putative glucoamylase
D: putative glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,16694
Polymers196,7214
Non-polymers5,44590
Water22,4471246
1
A: putative glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,14333
Polymers49,1801
Non-polymers1,96332
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: putative glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,55824
Polymers49,1801
Non-polymers1,37823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: putative glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,37621
Polymers49,1801
Non-polymers1,19520
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: putative glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,08816
Polymers49,1801
Non-polymers90815
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.180, 71.760, 221.790
Angle α, β, γ (deg.)90.000, 92.300, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
112AA30 - 18830 - 188
212BB30 - 18830 - 188
312CC30 - 18830 - 188
412DD30 - 18830 - 188
123AA189189
223BB189189
323CC189189
423DD189189
132AA190 - 451190 - 451
232BB190 - 451190 - 451
332CC190 - 451190 - 451
432DD190 - 451190 - 451

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Components

#1: Protein
putative glucoamylase / Glucan 1,4-a-glucosidase / Conserved hypothetical exported protein


Mass: 49180.273 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis NCTC 9343 (bacteria)
Gene: YP_210071.1, BF0338 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LIB7
#2: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: K
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 84 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1246 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 23-451 OF THE FULL LENGTH PROTEIN.

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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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 15.8% polyethylene glycol 3350, 0.1M potassium fluoride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97929,0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 3, 2008 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979291
30.97921
ReflectionResolution: 2.12→29.591 Å / Num. obs: 102011 / % possible obs: 90.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.102 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.54
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.12-2.20.4091.52307018064184.4
2.2-2.280.3621.82009915721185.3
2.28-2.390.29322407118820187.1
2.39-2.510.252.42211017221188.8
2.51-2.670.2162.82413018770190.3
2.67-2.880.1533.82445718957191.6
2.88-3.160.1055.52379618426193.8
3.16-3.620.0658.42537619543194.7
3.62-4.550.04512.22522219239195
4.55-29.5910.03713.42604919663195.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.12→29.591 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.93 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 9.831 / SU ML: 0.133 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.221 / ESU R Free: 0.182
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. POTASSIUM, ETHYLENE GLYCOL AND CHLORIDE, PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS, WERE MODELED INTO THE STRUCTURE. 5. THE CIS PEPTIDES BETWEEN 222-223 ARE SUPPORTED BY WELL DEFINED DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 5086 5 %RANDOM
Rwork0.158 ---
obs0.161 101993 98.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.62 Å2 / Biso mean: 26.572 Å2 / Biso min: 5.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å2-0.16 Å2
2--0.91 Å20 Å2
3----1.11 Å2
Refinement stepCycle: LAST / Resolution: 2.12→29.591 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13458 0 342 1246 15046
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02214270
X-RAY DIFFRACTIONr_bond_other_d0.0020.029893
X-RAY DIFFRACTIONr_angle_refined_deg1.3961.94119248
X-RAY DIFFRACTIONr_angle_other_deg0.939323765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.99951716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2423.456709
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.407152113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9181582
X-RAY DIFFRACTIONr_chiral_restr0.0820.21869
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216046
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023128
X-RAY DIFFRACTIONr_nbd_refined0.2070.22882
X-RAY DIFFRACTIONr_nbd_other0.1940.210200
X-RAY DIFFRACTIONr_nbtor_refined0.1850.26722
X-RAY DIFFRACTIONr_nbtor_other0.0860.26614
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.2946
X-RAY DIFFRACTIONr_metal_ion_refined0.1480.27
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2460.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1770.230
X-RAY DIFFRACTIONr_mcbond_it1.35138392
X-RAY DIFFRACTIONr_mcbond_other0.49633484
X-RAY DIFFRACTIONr_mcangle_it2.275513383
X-RAY DIFFRACTIONr_scbond_it4.19685994
X-RAY DIFFRACTIONr_scangle_it5.629115849
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2441TIGHT POSITIONAL0.060.08
2B2441TIGHT POSITIONAL0.070.08
3C2441TIGHT POSITIONAL0.060.08
4D2441TIGHT POSITIONAL0.060.08
1A3105MEDIUM POSITIONAL0.190.5
2B3105MEDIUM POSITIONAL0.210.5
3C3105MEDIUM POSITIONAL0.230.5
4D3105MEDIUM POSITIONAL0.190.5
1A18LOOSE POSITIONAL1.065
2B18LOOSE POSITIONAL1.175
3C18LOOSE POSITIONAL3.155
4D18LOOSE POSITIONAL0.965
1A2441TIGHT THERMAL0.51
2B2441TIGHT THERMAL0.471
3C2441TIGHT THERMAL0.431
4D2441TIGHT THERMAL0.451
1A3105MEDIUM THERMAL1.082
2B3105MEDIUM THERMAL1.032
3C3105MEDIUM THERMAL0.972
4D3105MEDIUM THERMAL12
1A18LOOSE THERMAL2.3810
2B18LOOSE THERMAL2.6810
3C18LOOSE THERMAL0.8910
4D18LOOSE THERMAL1.8610
LS refinement shellResolution: 2.12→2.175 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 358 -
Rwork0.215 6952 -
all-7310 -
obs--95.77 %
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)
10.2747-0.064-0.10530.5110.11160.5195-0.0172-0.0521-0.04580.03940.02080.03470.0295-0.0122-0.0036-0.0737-0.0085-0.0136-0.10230.0052-0.047714.467314.8976129.7244
20.4632-0.12490.10560.3265-0.19561.0218-0.0207-0.05430.02440.05820.00680.0086-0.15550.02780.0139-0.0453-0.0151-0.0016-0.08080.0016-0.0326-15.424747.1174146.5273
30.95890.1421-0.29950.4862-0.18121.6108-0.0230.1633-0.1643-0.15340.0201-0.00640.32470.02060.00290.03180.0312-0.00290.0291-0.0336-0.01469.27278.5469186.5065
40.41460.00530.0330.34910.09280.8336-0.0207-0.02680.1126-0.0045-0.0089-0.003-0.1016-0.12320.0296-0.05780.03280.004-0.0125-0.027-0.0165-19.052141.6894201.3881
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 451
2X-RAY DIFFRACTION2B30 - 451
3X-RAY DIFFRACTION3C30 - 451
4X-RAY DIFFRACTION4D30 - 451

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