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- PDB-3h3l: Crystal structure of PUTATIVE SUGAR HYDROLASE (YP_001304206.1) fr... -

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Entry
Database: PDB / ID: 3h3l
TitleCrystal structure of PUTATIVE SUGAR HYDROLASE (YP_001304206.1) from Parabacteroides distasonis ATCC 8503 at 1.59 A resolution
ComponentsPUTATIVE SUGAR HYDROLASE
KeywordsHYDROLASE / YP_001304206.1 / PUTATIVE SUGAR HYDROLASE / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Domain of Unknown Function (DUF1080) / unknown function
Function / homology3-keto-disaccharide hydrolase / 3-keto-disaccharide hydrolase / Exo-inulinase; domain 1 / Jelly Rolls / Sandwich / Mainly Beta / DUF1080 domain-containing protein
Function and homology information
Biological speciesParabacteroides distasonis ATCC 8503 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.59 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of PUTATIVE SUGAR HYDROLASE (YP_001304206.1) from Parabacteroides distasonis ATCC 8503 at 1.59 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 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 / 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_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 SUGAR HYDROLASE
B: PUTATIVE SUGAR HYDROLASE
C: PUTATIVE SUGAR HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4156
Polymers83,0493
Non-polymers3663
Water8,791488
1
A: PUTATIVE SUGAR HYDROLASE
hetero molecules

A: PUTATIVE SUGAR HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6104
Polymers55,3662
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2320 Å2
ΔGint-9 kcal/mol
Surface area19080 Å2
MethodPISA
2
B: PUTATIVE SUGAR HYDROLASE
C: PUTATIVE SUGAR HYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6104
Polymers55,3662
Non-polymers2442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-9 kcal/mol
Surface area18410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.259, 117.259, 118.068
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A37 - 270
2115B37 - 270
3115C37 - 270

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Components

#1: Protein PUTATIVE SUGAR HYDROLASE


Mass: 27682.914 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis ATCC 8503 (bacteria)
Gene: BDI_2876, YP_001304206.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LFX0
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE THE CONSTRUCT (RESIDUES 31-270) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. ...SEQUENCE THE CONSTRUCT (RESIDUES 31-270) 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: 2.44 Å3/Da / Density % sol: 49.66 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2000M Na2Ci, 30.0000% PEG-400, 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: 0.91837,0.97905,0.97839
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 18, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979051
30.978391
ReflectionResolution: 1.59→29.311 Å / Num. obs: 107246 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 23.046 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 16.59
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.59-1.650.011.816830222016198.5
1.65-1.710.012.414571518967198.3
1.71-1.790.013.316573121445198
1.79-1.880.015.415463519888197.7
1.88-20.018.616624821241197.4
2-2.160.0114.116808921332197
2.16-2.370.0120.715774519844196.4
2.37-2.720.0126.616728120838195.8
2.72-3.420.0137.116093919945194.7
3.42-29.3110.0148.316088219770192.3

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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: 1.59→29.311 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 2.875 / SU ML: 0.051 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.078 / ESU R Free: 0.074
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. 4.2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL (TRS) FROM THE CRYSTALLIZATION SOLUTION WAS USED AS A BUFFER. ELECTRON DENSITY WAS POOR FOR SOME REGIONS OF THE STRUCTURE INCLUDING PORTIONS OF THE N-TERMINI, RESIDUES B91-B95, AND C88-C95 THEREFORE, THESE REGIONS WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.185 5379 5 %RANDOM
Rwork0.17 ---
obs0.17 107212 96.62 %-
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: 84.47 Å2 / Biso mean: 36.734 Å2 / Biso min: 18.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å20 Å2
2--0.43 Å20 Å2
3----0.87 Å2
Refinement stepCycle: LAST / Resolution: 1.59→29.311 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5418 0 24 488 5930
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0225834
X-RAY DIFFRACTIONr_bond_other_d0.0040.024018
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9477956
X-RAY DIFFRACTIONr_angle_other_deg1.3239796
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5425752
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.99924.533289
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.85715966
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7541528
X-RAY DIFFRACTIONr_chiral_restr0.0990.2800
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026644
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021230
X-RAY DIFFRACTIONr_nbd_refined0.1770.31022
X-RAY DIFFRACTIONr_nbd_other0.1570.34186
X-RAY DIFFRACTIONr_nbtor_refined0.1790.52873
X-RAY DIFFRACTIONr_nbtor_other0.0840.52975
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.5797
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1350.360
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.554
X-RAY DIFFRACTIONr_mcbond_it1.18823595
X-RAY DIFFRACTIONr_mcbond_other0.37321434
X-RAY DIFFRACTIONr_mcangle_it1.96345688
X-RAY DIFFRACTIONr_scbond_it3.10362610
X-RAY DIFFRACTIONr_scangle_it4.40782232
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1271MEDIUM POSITIONAL0.170.5
2B1271MEDIUM POSITIONAL0.20.5
3C1271MEDIUM POSITIONAL0.150.5
1A1543LOOSE POSITIONAL0.225
2B1543LOOSE POSITIONAL0.265
3C1543LOOSE POSITIONAL0.235
1A1271MEDIUM THERMAL1.012
2B1271MEDIUM THERMAL1.172
3C1271MEDIUM THERMAL1.262
1A1543LOOSE THERMAL1.4810
2B1543LOOSE THERMAL1.610
3C1543LOOSE THERMAL1.7610
LS refinement shellResolution: 1.587→1.629 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 426 -
Rwork0.223 7544 -
all-7970 -
obs--97.97 %
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)
11.6650.8393-0.53741.49970.00032.3977-0.07840.0985-0.1169-0.11560.04670.09360.3115-0.11170.0317-0.1325-0.0161-0.0401-0.2121-0.0089-0.146627.47764.07125.958
22.3430.46620.65421.2257-0.2671.65230.01860.18850.12430.0036-0.0925-0.27740.01220.28270.0738-0.2249-0.00280.0114-0.15250.0468-0.085843.03826.80133.831
32.3432-0.39120.72721.6279-1.30763.69260.1723-0.0037-0.147-0.35910.15960.32070.4742-0.4379-0.3319-0.1295-0.062-0.0763-0.17030.0551-0.121210.85916.53221.623
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 270
2X-RAY DIFFRACTION2B37 - 270
3X-RAY DIFFRACTION3C40 - 270

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