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- PDB-3u1x: Crystal structure of a putative glycosyl hydrolase (BDI_1869) fro... -

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Basic information

Entry
Database: PDB / ID: 3u1x
TitleCrystal structure of a putative glycosyl hydrolase (BDI_1869) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution
Componentsputative glycosyl hydrolase
KeywordsHYDROLASE / glycosyl hydrolysis / carbohydrate metabolism / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology3-keto-disaccharide hydrolase / 3-keto-disaccharide hydrolase / Exo-inulinase; domain 1 / Jelly Rolls / Sandwich / Mainly Beta / TRIETHYLENE GLYCOL / DUF1080 domain-containing protein
Function and homology information
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative glycosyl hydrolase (BDI_1869) from Parabacteroides distasonis ATCC 8503 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: putative glycosyl hydrolase
B: putative glycosyl hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,4954
Polymers54,1952
Non-polymers3002
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-4 kcal/mol
Surface area20350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.690, 41.214, 77.324
Angle α, β, γ (deg.)92.980, 91.640, 117.970
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A30 - 257
2115B30 - 257

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Components

#1: Protein putative glycosyl hydrolase


Mass: 27097.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_1869 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6LD40
#2: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 24-258 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 Å3/Da / Density % sol: 38.59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1M MES pH 6, 30% polyethylene glycol 6000, 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: 0.97907
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 5, 2011
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 1.7→27.459 Å / Num. obs: 44063 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 18.403 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.760.5211.5815094764483
1.76-1.830.3832.217087857093.7
1.83-1.910.268316765839794
1.91-2.020.1744.618958950393.7
2.02-2.140.1196.616651834494.6
2.14-2.310.088917887895994.5
2.31-2.540.0711.217284866695
2.54-2.90.04815.617147859394.6
2.9-3.660.02426.517616883594.3
3.660.0173817565880294.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
REFMAC5.6.0117refinement
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→27.459 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.23 / SU B: 4.299 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.108
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. PEG (PGE) MODELED ARE PRESENT IN CRYO CONDITION. 4. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1967 2234 5.1 %RANDOM
Rwork0.1578 ---
obs0.1597 44063 95.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 90.68 Å2 / Biso mean: 22.8359 Å2 / Biso min: 7.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0.03 Å2-0.31 Å2
2--0.39 Å20.04 Å2
3----0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3581 0 20 431 4032
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223762
X-RAY DIFFRACTIONr_bond_other_d0.0020.022557
X-RAY DIFFRACTIONr_angle_refined_deg1.3461.9275094
X-RAY DIFFRACTIONr_angle_other_deg0.86436229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3115452
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.13425.492193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.98715624
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.959154
X-RAY DIFFRACTIONr_chiral_restr0.0890.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024230
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02786
X-RAY DIFFRACTIONr_bond_it2.853.3623762
X-RAY DIFFRACTIONr_bond_other0.6213.4812557
X-RAY DIFFRACTIONr_angle_it4.3326.125086
X-RAY DIFFRACTIONr_angle_others2.6126.5216229
X-RAY DIFFRACTIONr_torsion_it7.59913.3251273
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1258MEDIUM POSITIONAL0.270.5
1675LOOSE POSITIONAL0.485
1258MEDIUM THERMAL3.372
1675LOOSE THERMAL3.8310
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 169 -
Rwork0.245 2633 -
all-2802 -
obs--81.5 %
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)
10.47850.0432-0.01480.20870.05880.2557-0.0059-0.0289-0.0297-0.00280.00660.0030.0160.0126-0.00060.0178-0.0021-0.00770.0039-0.00070.02512.7329-0.890753.2845
20.95730.26740.05260.4442-0.25751.0668-0.0077-0.0615-0.05250.04190.0007-0.00970.0290.01680.0070.03560.01370.00050.0306-0.00510.0181-11.9598-6.141990.0584
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 258
2X-RAY DIFFRACTION2B30 - 258

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