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- PDB-4qhx: Crystal structure of a putative two-domain sugar hydrolase (BACCA... -

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Basic information

Entry
Database: PDB / ID: 4qhx
TitleCrystal structure of a putative two-domain sugar hydrolase (BACCAC_02064) from Bacteroides caccae ATCC 43185 at 1.80 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two domain protein / galactose-binding domain-like fold / concanavalin A-like fold / PF11958 family / DUF3472 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF3472 / Domain of unknown function DUF5077 / Domain of unknown function (DUF3472) / Domain of unknown function (DUF5077) / DI(HYDROXYETHYL)ETHER / DUF5077 domain-containing protein
Function and homology information
Biological speciesBacteroides caccae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACCAC_02064) from Bacteroides caccae ATCC 43185 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 29, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 23, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,82921
Polymers45,9661
Non-polymers1,86320
Water7,620423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,48863
Polymers137,8993
Non-polymers5,58960
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area14360 Å2
ΔGint-415 kcal/mol
Surface area51600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.042, 110.042, 105.557
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-504-

SO4

21A-504-

SO4

31A-507-

SO4

41A-507-

SO4

51A-653-

HOH

61A-710-

HOH

DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized protein


Mass: 45966.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae (bacteria) / Strain: ATCC 43185 / Gene: BACCAC_02064 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A5ZGP5

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Non-polymers , 5 types, 443 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 19-418 OF 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: 2.68 Å3/Da / Density % sol: 54.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.16M ammonium sulfate, 20.0% Glycerol, 20.0% polyethylene glycol 4000, 0.1M sodium acetate pH 4.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97934,0.95369,0.97913
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 4, 2014
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
10.979341
20.953691
30.979131
ReflectionResolution: 1.8→29.643 Å / Num. obs: 43818 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.126 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 9.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.8-1.860.5031.615048774291.8
1.86-1.940.3662.217857919297.7
1.94-2.030.243.317137880597.7
2.03-2.130.1684.615779811198
2.13-2.270.135.917870917498.3
2.27-2.440.17.516398840498.1
2.44-2.690.0721017183880897.3
2.69-3.070.0514.416155828896.1
3.07-3.870.0342016296836793.9
3.870.02623.416813857796.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMAC5.8.0069refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→29.643 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.964 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 4.846 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.1
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 4. 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. 5. GLYCEROL (GOL), SULFATE (SO4), CHLORIDE (CL), AND PEG (PEG) MODELED WERE PRESENT IN CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1789 2198 5 %RANDOM
Rwork0.1492 ---
obs0.1507 43818 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 83.19 Å2 / Biso mean: 29.4797 Å2 / Biso min: 17.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å2-0 Å2
2--0.51 Å2-0 Å2
3----1.65 Å2
Refinement stepCycle: LAST / Resolution: 1.8→29.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3230 0 109 423 3762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223540
X-RAY DIFFRACTIONr_bond_other_d0.0020.023236
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.964797
X-RAY DIFFRACTIONr_angle_other_deg0.80437493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4795436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11724.045178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41215591
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7511520
X-RAY DIFFRACTIONr_chiral_restr0.0960.2468
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214010
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02860
X-RAY DIFFRACTIONr_mcbond_it1.1982.0521637
X-RAY DIFFRACTIONr_mcbond_other1.1972.0511636
X-RAY DIFFRACTIONr_mcangle_it1.7413.0732054
LS refinement shellResolution: 1.802→1.849 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 163 -
Rwork0.25 3043 -
all-3206 -
obs--99.13 %
Refinement TLS params.Method: refined / Origin x: 35.6438 Å / Origin y: 7.8641 Å / Origin z: 111.1545 Å
111213212223313233
T0.036 Å20.004 Å20.007 Å2-0.0198 Å2-0.0127 Å2--0.0291 Å2
L0.5697 °2-0.0535 °2-0.2973 °2-0.1775 °2-0.0114 °2--0.3706 °2
S0.0069 Å °0.0323 Å °0.0718 Å °0.0193 Å °0.0167 Å °-0.0206 Å °-0.0473 Å °-0.0262 Å °-0.0236 Å °

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