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- PDB-8u01: Crystal Structure of the Glycoside Hydrolase Family 2 TIM Barrel-... -

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Basic information

Entry
Database: PDB / ID: 8u01
TitleCrystal Structure of the Glycoside Hydrolase Family 2 TIM Barrel-domain Containing Protein from Phocaeicola plebeius
ComponentsGlycosyl hydrolase family 2, sugar binding domain protein
KeywordsHYDROLASE / beta galactosidase / TIM barrel Structural Genomics / Midwest Center for Structural Genomics
Function / homology
Function and homology information


beta-galactosidase / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
: / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / D-tagatose / beta-galactosidase
Similarity search - Component
Biological speciesPhocaeicola plebeius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3 Å
AuthorsKim, Y. / Joachimiak, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Glycoside Hydrolase Family 2 TIM Barrel-domain Containing Protein from Phocaeicola plebeius
Authors: Kim, Y. / Joachimiak, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionAug 28, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.2Nov 13, 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: Glycosyl hydrolase family 2, sugar binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,25741
Polymers104,0011
Non-polymers3,25640
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-25 kcal/mol
Surface area33950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.110, 230.110, 230.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
Space group name HallP4bd2ab3
Symmetry operation#1: x,y,z
#2: x+1/4,-z+1/4,y+3/4
#3: x+3/4,z+1/4,-y+1/4
#4: z+3/4,y+1/4,-x+1/4
#5: -z+1/4,y+3/4,x+1/4
#6: -y+1/4,x+3/4,z+1/4
#7: y+1/4,-x+1/4,z+3/4
#8: z,x,y
#9: y,z,x
#10: -y+1/2,-z,x+1/2
#11: z+1/2,-x+1/2,-y
#12: -y,z+1/2,-x+1/2
#13: -z+1/2,-x,y+1/2
#14: -z,x+1/2,-y+1/2
#15: y+1/2,-z+1/2,-x
#16: x+1/2,-y+1/2,-z
#17: -x,y+1/2,-z+1/2
#18: -x+1/2,-y,z+1/2
#19: y+3/4,x+1/4,-z+1/4
#20: -y+3/4,-x+3/4,-z+3/4
#21: z+1/4,-y+1/4,x+3/4
#22: -z+3/4,-y+3/4,-x+3/4
#23: -x+1/4,z+3/4,y+1/4
#24: -x+3/4,-z+3/4,-y+3/4
Components on special symmetry positions
IDModelComponents
11A-1019-

PEG

21A-1231-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Glycosyl hydrolase family 2, sugar binding domain protein


Mass: 104001.133 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Phocaeicola plebeius (bacteria) / Gene: BACPLE_01374 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): gold / References: UniProt: B5CXD3
#9: Sugar ChemComp-TAG / D-tagatose


Type: D-saccharide / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION

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Non-polymers , 8 types, 228 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 4.93 Å3/Da / Density % sol: 75.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium chloride, 0.1 M HEPES, pH 7.5, 30% v/v PEG400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3→72.8 Å / Num. obs: 42107 / % possible obs: 100 % / Redundancy: 26 % / Biso Wilson estimate: 44.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.137 / Rpim(I) all: 0.027 / Rrim(I) all: 0.139 / Net I/σ(I): 28.9
Reflection shellResolution: 3→3.05 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.524 / Mean I/σ(I) obs: 7.5 / Num. unique obs: 2039 / CC1/2: 0.974 / Rpim(I) all: 0.105 / Rrim(I) all: 0.534 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
xia2data scaling
HKL-3000phasing
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 3→69.38 Å / SU ML: 0.2713 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.1531
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1861 2129 5.06 %
Rwork0.1534 39908 -
obs0.1551 42037 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.3 Å2
Refinement stepCycle: LAST / Resolution: 3→69.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7177 0 207 189 7573
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317588
X-RAY DIFFRACTIONf_angle_d0.564510222
X-RAY DIFFRACTIONf_chiral_restr0.04271071
X-RAY DIFFRACTIONf_plane_restr0.00451310
X-RAY DIFFRACTIONf_dihedral_angle_d13.94082774
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.070.30491430.23582591X-RAY DIFFRACTION99.27
3.07-3.150.24931480.20882599X-RAY DIFFRACTION99.96
3.15-3.230.29761460.19542612X-RAY DIFFRACTION99.96
3.23-3.330.22151280.19472627X-RAY DIFFRACTION100
3.33-3.440.24891300.18492637X-RAY DIFFRACTION100
3.44-3.560.19861340.17852609X-RAY DIFFRACTION99.89
3.56-3.70.2221590.16652621X-RAY DIFFRACTION99.93
3.7-3.870.18971380.14242623X-RAY DIFFRACTION99.93
3.87-4.070.16341340.13242643X-RAY DIFFRACTION100
4.07-4.330.1671440.11872670X-RAY DIFFRACTION100
4.33-4.660.14961490.10782641X-RAY DIFFRACTION100
4.66-5.130.11871460.11122670X-RAY DIFFRACTION99.96
5.13-5.880.14741160.1322735X-RAY DIFFRACTION100
5.88-7.40.17491460.16282743X-RAY DIFFRACTION100
7.4-69.380.16371680.16992887X-RAY DIFFRACTION99.41
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)
10.4596153481110.1017871577590.2599277210910.739079239967-0.05448887156480.726000414968-0.0235204340021-0.004218448440580.0924978424743-0.0749158598298-0.00650241050105-0.0809162369206-0.138245656729-0.0337362850740.03561852414070.2850650800320.05850736681110.03104036044190.261517718947-0.03903410077960.326268552111123.35183834127.753167452141.1186240384
28.685095610777.072727322350.4528207913396.341827286550.01639265352630.6028271888740.176666810177-0.299884127252-0.09116402082860.321465901693-0.201189080092-0.2524323409670.0592838365304-0.06108092140070.0231730077160.3052496146360.112943088155-0.00855765622630.268599215221-0.03041275215580.311408033225135.87992197916.68219466768.4472753029
30.8921022221270.07944718408170.3333223862470.6386419045110.1418266068490.7413513691210.0157527711301-0.01915008768990.01534183850580.0047072862172-0.0251173741737-0.0593378149007-0.0106786588458-0.02845298887140.00989437956380.2482694382770.04768712383710.0022543159840.211039019927-0.03613956888380.225534500389117.1857352314.1114876559742.9131023134
43.773930218642.142520055791.512870486563.116775663441.148602120573.383025716120.182241694517-0.444601088335-0.2618528599510.102606181773-0.1163798916740.04201555281270.223358378397-0.435130152776-0.04051281378090.2851752308240.02514258871690.04142933350930.2590300318070.002791242292880.21920952960899.8318545405-19.353605810751.8029202276
52.831390167560.5771531810892.842426504331.158691272410.6705960995734.069546422290.1270026853290.110584663242-0.159535675506-0.09288011166340.07055157277790.2879794737220.233067942755-0.386207935526-0.3169717478210.2361589982970.009718516175090.0008042352935920.203505453776-0.0453465476210.36500785753687.1354275336-17.476280464820.2580236347
61.23445427341.76657260070.2951283457842.665976189630.8534721926741.77033408403-0.08525151811540.01193807658790.129179102535-0.1462972042180.03149533959290.227986464797-0.104119649512-0.247986111010.07381024857040.2009608239150.0302982253752-0.01361731080020.24464283848-0.06417873992760.26527869376994.0761554891-5.3557359268726.5242448043
72.636889583381.155139086370.8834251451973.86104035410.156338995592.64772465634-0.089964038708-0.06189171044710.312164113314-0.326804146774-0.0820732110260.40174829337-0.0721523797929-0.5707896806670.1507821018610.2842491287550.00257045347563-0.02355803500440.342082466186-0.09278115316240.30248874114683.3157484464-15.211950619119.240188616
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 213 )-2 - 2131 - 217
22chain 'A' and (resid 214 through 274 )214 - 274218 - 278
33chain 'A' and (resid 275 through 603 )275 - 603279 - 607
44chain 'A' and (resid 604 through 704 )604 - 704608 - 708
55chain 'A' and (resid 705 through 765 )705 - 765709 - 766
66chain 'A' and (resid 766 through 844 )766 - 844767 - 845
77chain 'A' and (resid 845 through 908 )845 - 908846 - 909

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