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- PDB-4jrl: Crystal structure of a putative glycoside hydrolase (BACOVA_00087... -

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Basic information

Entry
Database: PDB / ID: 4jrl
TitleCrystal structure of a putative glycoside hydrolase (BACOVA_00087) from Bacteroides ovatus ATCC 8483 at 2.10 A resolution
Componentsputative glycoside hydrolase
KeywordsHYDROLASE / Galactose-binding domain-like / PF13201 family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


BT2081, beta-jelly-roll domain / Immunoglobulin-like - #2340 / Putative carbohydrate metabolism domain / Putative carbohydrate metabolism domain superfamily / Putative carbohydrate metabolism domain / Jelly Rolls / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PCMD domain-containing protein
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative glycoside hydrolase (BACOVA_00087) from Bacteroides ovatus ATCC 8483 at 2.10 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: putative glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,3428
Polymers39,8431
Non-polymers5007
Water2,990166
1
A: putative glycoside hydrolase
hetero molecules

A: putative glycoside hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,68516
Polymers79,6852
Non-polymers1,00014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
Buried area4020 Å2
ΔGint-65 kcal/mol
Surface area32440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.880, 133.880, 127.498
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-403-

SO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein putative glycoside hydrolase /


Mass: 39842.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: ZP_02063147.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7LQL7

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Non-polymers , 5 types, 173 molecules

#2: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


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


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS CONSTRUCT (RESIDUES 21-375) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 21-375) 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: 2.76 Å3/Da / Density % sol: 55.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1M bicine pH 9, 2.4M ammonium sulfate, 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: 0.91837,0.97932
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 24, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979321
ReflectionResolution: 2.1→28.711 Å / Num. obs: 25691 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 33.623 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 10.21
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.1-2.170.8621.616286460599
2.17-2.260.7218322517199.7
2.26-2.360.6142.316849482699.5
2.36-2.490.4962.817367517599.4
2.49-2.640.323416228476699.6
2.64-2.850.2415.618434516199.6
2.85-3.130.1419.217070484399.6
3.13-3.590.07316.117182503299.4
3.59-4.510.04226.817508491399.7
4.510.03331.417326501199.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012data scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→28.711 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 8.247 / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.163
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. SODIUM (NA), CHLORIDE (CL), AND GLYCEROL (GOL) FROM THE CRYSTALLIZATION/CRYO CONDITIONS HAVE BEEN MODELED INTO THE STRUCTURE.4.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 6. AN UNKNOWN ION (UNX) HAS BEEN MODELED BASED ON A PEAK IN THE ANOMALOUS DIFFERENCE FOURIER MAP. THE ION LIKELY CO-PURIFIED WITH THE PROTEIN. X-RAY FLUORESCENCE EXCITATION SPECTRA WERE INCONCLUSIVE IN DETERMINING THE METAL IDENTITY WITH MINOR PEAKS FOR ZN, CU, FE AND CA. FOR THE PURPOSE OF REFINEMENT THE UNX ATOM TYPE X WAS ASSIGNED SCATTERING FACTORS EQUIVALENT TO CA WHICH GAVE A REASONABLE FIT TO THE OBSERVED DENSITY. 7. THE SCATTERING FACTORS FOR SULFUR, CHLORINE, SELENIUM AND THE UNKNOWN X ATOMS WERE ADJUSTED BY REFMAC 5.7.0032 TO ACCOUNT FOR ANOMALOUS DISPERSION BASED ON THE WAVELENGTH 0.91837 A (S F'= 0.16, CL F'= 0.19, SE F'= -1.94, X F'= 0.27). THE CROMER MANN VALUES LISTED IN THE CIF VERSION OF THE FILE INCLUDE THIS CORRECTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2202 1307 5.1 %RANDOM
Rwork0.1707 ---
obs0.1731 25691 99.73 %-
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: 110.19 Å2 / Biso mean: 41.5498 Å2 / Biso min: 20.51 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20.65 Å2-0 Å2
2--0.65 Å2-0 Å2
3----2.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→28.711 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 31 166 2914
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022818
X-RAY DIFFRACTIONr_bond_other_d0.0010.022614
X-RAY DIFFRACTIONr_angle_refined_deg1.7821.9693818
X-RAY DIFFRACTIONr_angle_other_deg0.80336042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0995353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.97125.606132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.33715458
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.66158
X-RAY DIFFRACTIONr_chiral_restr0.1060.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023212
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02626
X-RAY DIFFRACTIONr_mcbond_it3.935.9921397
X-RAY DIFFRACTIONr_mcbond_other3.9245.9911396
X-RAY DIFFRACTIONr_mcangle_it5.0711.1981746
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 86 -
Rwork0.233 1789 -
all-1875 -
obs--99.26 %
Refinement TLS params.Method: refined / Origin x: 0.357 Å / Origin y: 32.233 Å / Origin z: 19.272 Å
111213212223313233
T0.0186 Å20.0138 Å20.0104 Å2-0.0622 Å2-0.0077 Å2--0.0652 Å2
L0.5632 °20.2146 °20.3081 °2-0.4978 °20.0519 °2--0.8964 °2
S0.0012 Å °-0.0269 Å °-0.0874 Å °0.045 Å °0.0429 Å °-0.1227 Å °0.0078 Å °0.1192 Å °-0.0441 Å °

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