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- PDB-3s5q: Crystal structure of a putative glycosyl hydrolase (BDI_2473) fro... -

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Basic information

Entry
Database: PDB / ID: 3s5q
TitleCrystal structure of a putative glycosyl hydrolase (BDI_2473) from Parabacteroides distasonis ATCC 8503 at 1.85 A resolution
ComponentsPutative glycosylhydrolase
KeywordsHYDROLASE / Concanavalin A-like lectins/glucanases / 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 / hydrolase activity / Jelly Rolls / Sandwich / Mainly Beta / IODIDE ION / Putative glycosylhydrolase
Function and homology information
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical Glycosyl hydrolase (BDI_2473) from Parabacteroides distasonis ATCC 8503 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 24, 2014Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative glycosylhydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,49510
Polymers24,7421
Non-polymers7539
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.062, 60.473, 77.221
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative glycosylhydrolase


Mass: 24742.064 Da / Num. of mol.: 1 / Fragment: sequence database residues 29-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / DSM 20701 / NCTC 11152 / Gene: BDI_2473 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6LES9
#2: Chemical ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: I
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (RESIDUES 29-223) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 1.94 Å3/Da / Density % sol: 36.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.200M NH4I, 20.00% PEG-3350, No Buffer pH 6.2, 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: 0.97954,0.91837,0.97874
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 7, 2009
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979541
20.918371
30.978741
ReflectionResolution: 1.85→36.25 Å / Num. obs: 16569 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 3.98 % / Biso Wilson estimate: 20.25 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.41
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.85-1.923.990.6832.16715168496.1
1.92-1.990.5212.85932146996.3
1.99-2.080.3743.86565162996.7
2.08-2.190.34.76587162396.8
2.19-2.330.2395.96740166496.8
2.33-2.510.1767.76698165897.6
2.51-2.760.12910.26652165797.5
2.76-3.160.07915.36712167898.2
3.16-3.980.04225.86647169197.6
3.98-36.250.03332.36742181697.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJanuary 30data scaling
REFMAC5.5.0110refinement
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→36.25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.588 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.136
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. A MET- ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 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. ANOMALOUS DIFFERENCE FOURIERS SUPPORT THE MODELING OF IODIDE (IOD) IONS. 6. 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2018 854 5.2 %RANDOM
Rwork0.1693 ---
obs0.1711 16554 97.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 60.5 Å2 / Biso mean: 25.9466 Å2 / Biso min: 12.68 Å2
Baniso -1Baniso -2Baniso -3
1-2.38 Å20 Å20 Å2
2---1.43 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 1.85→36.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1728 0 27 187 1942
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211831
X-RAY DIFFRACTIONr_bond_other_d0.0010.021225
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.9172491
X-RAY DIFFRACTIONr_angle_other_deg0.89532996
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8225224
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40725.21792
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.65315295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.915154
X-RAY DIFFRACTIONr_chiral_restr0.0930.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02361
X-RAY DIFFRACTIONr_mcbond_it0.7641.51076
X-RAY DIFFRACTIONr_mcbond_other0.2211.5438
X-RAY DIFFRACTIONr_mcangle_it1.28921750
X-RAY DIFFRACTIONr_scbond_it2.1623755
X-RAY DIFFRACTIONr_scangle_it3.2144.5735
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 68 -
Rwork0.259 1128 -
all-1196 -
obs--95.83 %
Refinement TLS params.Method: refined / Origin x: 29.802 Å / Origin y: 24.844 Å / Origin z: 55.979 Å
111213212223313233
T0.0152 Å20.0121 Å2-0.0137 Å2-0.0881 Å20.0028 Å2--0.085 Å2
L0.2823 °20.2395 °20.2111 °2-0.7913 °20.7159 °2--1.543 °2
S0.0128 Å °0.0274 Å °-0.0477 Å °0.0834 Å °0.0468 Å °-0.1047 Å °0.1412 Å °0.0824 Å °-0.0596 Å °

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