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- PDB-4gl3: Crystal structure of a putative glucoamylase (BACUNI_03963) from ... -

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Basic information

Entry
Database: PDB / ID: 4gl3
TitleCrystal structure of a putative glucoamylase (BACUNI_03963) from Bacteroides uniformis ATCC 8492 at 2.01 A resolution
Componentsputative glucoamylase
KeywordsHYDROLASE / PF10091 family protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


Glycoside hydrolase 144 (GH144) / Uncharacterised conserved protein UCP028431 / Glycoamylase-like, conserved domain / Putative glucoamylase / Glycosyltransferase / Alpha/alpha barrel / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Glycoamylase-like domain-containing protein
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.01 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative glucoamylase (BACUNI_03963) from Bacteroides uniformis ATCC 8492 at 2.01 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
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 30, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4057
Polymers48,7951
Non-polymers6116
Water7,152397
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.568, 121.568, 267.888
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-854-

HOH

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Components

#1: Protein putative glucoamylase


Mass: 48794.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Strain: ATCC 8492 / Gene: BACUNI_03963 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7V8P4
#2: 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
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 27-449) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 27-449) 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: 3.9 Å3/Da / Density % sol: 68.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20.0% polyethylene glycol 300, 10.0% Glycerol, 5.0% polyethylene glycol 8000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.9792,0.97883
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.97921
30.978831
ReflectionResolution: 2.01→29.028 Å / Num. obs: 50890 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.23 % / Biso Wilson estimate: 28.41 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 8.97
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.01-2.080.8871.55328419570199.4
2.08-2.170.5912.44128610582199.7
2.17-2.260.4553.1347098953199.8
2.26-2.380.3384381079897199.8
2.38-2.530.2655376529929199.9
2.53-2.730.1946.5354559953199.5
2.73-30.1379.3384399691199.9
3-3.430.08714.1376339768199.8
3.43-4.320.05719.8346579770199
4.32-29.030.04424.1371729865199.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
REFMAC5.6.0117refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.01→29.028 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 4.666 / SU ML: 0.066 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.098
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 SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5.TRIS (TRS), GLYCEROL (GOL) AND POLYETHYLENE GLYCOL (PEG) FROM THE CRYSTALLIZATION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.1699 2580 5.1 %RANDOM
Rwork0.1412 ---
obs0.1427 50888 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 117.54 Å2 / Biso mean: 34.1577 Å2 / Biso min: 16.17 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20.78 Å20 Å2
2--1.56 Å20 Å2
3----2.34 Å2
Refinement stepCycle: LAST / Resolution: 2.01→29.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 40 397 3756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0193516
X-RAY DIFFRACTIONr_bond_other_d0.0010.022442
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.934759
X-RAY DIFFRACTIONr_angle_other_deg0.90435880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.145427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83223.37181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64715560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0271523
X-RAY DIFFRACTIONr_chiral_restr0.0910.2466
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213969
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02806
LS refinement shellResolution: 2.01→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 189 -
Rwork0.232 3372 -
all-3561 -
obs--99.47 %
Refinement TLS params.Method: refined / Origin x: 3.4668 Å / Origin y: 29.4419 Å / Origin z: 112.72 Å
111213212223313233
T0.0954 Å2-0.0106 Å2-0.014 Å2-0.0151 Å20.0216 Å2--0.0436 Å2
L0.5815 °20.2318 °20.0557 °2-1.4103 °2-0.2913 °2--1.2665 °2
S-0.0018 Å °0.0637 Å °0.1412 Å °-0.0506 Å °-0.0647 Å °0.0005 Å °-0.3142 Å °0.0756 Å °0.0665 Å °

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