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- PDB-4qt9: Crystal structure of a putative glucoamylase (BACCAC_03554) from ... -

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Basic information

Entry
Database: PDB / ID: 4qt9
TitleCrystal structure of a putative glucoamylase (BACCAC_03554) from Bacteroides caccae ATCC 43185 at 2.05 A resolution
Componentsputative glucoamylase
KeywordsHYDROLASE / PF10091 family / alpha/alpha toroid fold / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyUncharacterised conserved protein UCP028431 / Glycoside hydrolase 144 (GH144) / Glycoamylase-like, conserved domain / Putative glucoamylase / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha / ACETATE ION / Glycoamylase domain-containing protein
Function and homology information
Biological speciesBacteroides caccae ATCC 43185 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative glucoamylase (BACCAC_03554) from Bacteroides caccae ATCC 43185 at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: putative glucoamylase
B: putative glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,8237
Polymers100,4642
Non-polymers3585
Water8,665481
1
A: putative glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3503
Polymers50,2321
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: putative glucoamylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4724
Polymers50,2321
Non-polymers2403
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.925, 80.728, 90.752
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-698-

HOH

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Components

#1: Protein putative glucoamylase


Mass: 50232.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae ATCC 43185 (bacteria)
Gene: BACCAC_03554 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A5ZKV7
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 481 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (30-467) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (30-467) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.15 Å3/Da / Density % sol: 42.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M sodium acetate, 30.0% polyethylene glycol 4000, 0.1M tris hydrochloride pH 8.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97886,0.9793
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 17, 2013
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978861
20.97931
ReflectionResolution: 2.05→47.614 Å / Num. obs: 54536 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.44 Å2 / Rmerge(I) obs: 0.173 / Net I/σ(I): 7.01
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.05-2.120.8210.9671.925793522747261.06990.4
2.12-2.210.8830.7882.433118574057380.867100
2.21-2.310.9110.672.831053542154150.73899.9
2.31-2.430.940.5423.430995535853550.59699.9
2.43-2.580.9640.4174.231117538853860.459100
2.58-2.780.9770.3115.331740551355020.34299.8
2.78-3.060.990.21731448549954920.23299.9
3.06-3.50.9960.12410.431580553455230.13799.8
3.5-4.40.9980.07514.831397555655450.08399.8
4.40.9980.06816.532021588658400.07599.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012 BUILT=20130617data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.05→47.614 Å / Cor.coef. Fo:Fc: 0.9591 / Cor.coef. Fo:Fc free: 0.9412 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE EXPERIMENTAL (MAD) PHASES WERE USED AS RESTRAINTS DURING REF 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. ACETATE (ACT) AND TRIS BASE (TRS) FROM THE CRYSTALLIZATION SOLUT HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 2765 5.07 %RANDOM
Rwork0.1821 ---
obs0.184 54483 98.92 %-
Displacement parametersBiso max: 110 Å2 / Biso mean: 30.6885 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--1.8715 Å20 Å20 Å2
2--0.5614 Å20 Å2
3---1.3101 Å2
Refine analyzeLuzzati coordinate error obs: 0.253 Å
Refinement stepCycle: LAST / Resolution: 2.05→47.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6640 0 24 481 7145
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3100SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes165HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1070HARMONIC5
X-RAY DIFFRACTIONt_it7036HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion838SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8581SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7036HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9603HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion2.92
LS refinement shellResolution: 2.05→2.1 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 166 4.71 %
Rwork0.2037 3359 -
all0.2058 3525 -
obs--98.92 %
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)
10.76710.04890.18830.20630.05121.15910.0298-0.00220.033-0.0073-0.0150.003-0.042-0.0394-0.0148-0.1671-0.00330.00280.2261-0.0033-0.161775.910318.927347.4871
20.7216-0.0170.00360.1475-0.04870.89360.0292-0.01940.04220.0054-0.02470.0049-0.06120.0628-0.0045-0.15480.00220.00490.235-0.0019-0.1555105.40318.999788.6102
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|47 - 460 }A47 - 460
2X-RAY DIFFRACTION2{ B|48 - 460 }B48 - 460

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