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- PDB-3sql: Crystal Structure of Glycoside Hydrolase from Synechococcus -

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Basic information

Entry
Database: PDB / ID: 3sql
TitleCrystal Structure of Glycoside Hydrolase from Synechococcus
ComponentsGlycosyl hydrolase family 3
KeywordsHYDROLASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / TIM-barrel / alpha-beta-alpha sandwich / cytosol
Function / homology
Function and homology information


beta-N-acetylhexosaminidase / glycosyltransferase activity / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolase family 3 / Bacterial Glycosyl hydrolase family 3, C-terminal / Bacterial Glycosyl hydrolase family 3 C-terminal domain / : / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / TIM Barrel ...Glycosyl hydrolase family 3 / Bacterial Glycosyl hydrolase family 3, C-terminal / Bacterial Glycosyl hydrolase family 3 C-terminal domain / : / Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / DI(HYDROXYETHYL)ETHER / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsKim, Y. / Chhor, G. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Glycoside Hydrolase from Synechococcus
Authors: Kim, Y. / Chhor, G. / Bearden, J. / Joachimiak, A.
History
DepositionJul 5, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Glycosyl hydrolase family 3
B: Glycosyl hydrolase family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,54419
Polymers117,2152
Non-polymers1,32917
Water9,530529
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-119 kcal/mol
Surface area35700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.727, 128.727, 182.987
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-582-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glycosyl hydrolase family 3


Mass: 58607.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: PCC 7002 / Gene: SYNPCC7002_A0075 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: B1XLD2

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Non-polymers , 5 types, 546 molecules

#2: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.23 Å3/Da / Density % sol: 61.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Ammonium Acetate 0.1 M Bis-Tris:HCl pH 5.5 25% (w/v) PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 25, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 72242 / Num. obs: 72242 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 39.09 Å2 / Rsym value: 0.087 / Net I/σ(I): 8
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 3522 / Rsym value: 0.654 / % possible all: 96.4

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
BUCCANEERmodel building
PHENIX(phenix.refine: dev_761)refinement
HKL-3000data reduction
HKL-3000data scaling
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.25→43.106 Å / SU ML: 0.64 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.44 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 3639 5.06 %random
Rwork0.163 ---
all0.164 71963 --
obs0.164 71963 98.02 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.76 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso mean: 43.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.3978 Å20 Å2-0 Å2
2--3.3978 Å20 Å2
3----6.7956 Å2
Refinement stepCycle: LAST / Resolution: 2.25→43.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8033 0 78 529 8640
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.018589
X-RAY DIFFRACTIONf_angle_d1.29211758
X-RAY DIFFRACTIONf_dihedral_angle_d14.5793149
X-RAY DIFFRACTIONf_chiral_restr0.0961330
X-RAY DIFFRACTIONf_plane_restr0.0081547
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.25-2.27960.26471510.23672519267096
2.2796-2.31080.27951280.2252575271397
2.3108-2.34380.25831310.2212564269597
2.3438-2.37880.26111380.19092585272398
2.3788-2.4160.24581340.20912555268997
2.416-2.45560.25241290.19382594272397
2.4556-2.49790.24321490.18782560270998
2.4979-2.54340.23941320.17792614274698
2.5434-2.59230.23581260.17272601272798
2.5923-2.64520.24011310.18312593272498
2.6452-2.70270.22131270.17512611273898
2.7027-2.76550.25211310.18272602273398
2.7655-2.83470.27921380.17912631276998
2.8347-2.91130.22481470.17712599274698
2.9113-2.9970.21521700.17892574274498
2.997-3.09370.22191470.17322608275598
3.0937-3.20420.24331400.17942638277899
3.2042-3.33250.21791320.18712643277598
3.3325-3.48410.19911420.17632660280299
3.4841-3.66770.1921390.17012671281099
3.6677-3.89730.16771330.15422682281599
3.8973-4.1980.18261370.1342677281499
4.198-4.620.14111630.11352691285499
4.62-5.28750.13641470.12192701284899
5.2875-6.65780.18221450.1592748289399
6.6578-43.11360.1621520.15432828298096
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)
11.0073-0.1380.00060.63230.00891.39270.0888-0.04240.0120.0195-0.0631-0.1115-0.03830.2889-0.04010.1954-0.0668-0.01340.28560.03390.202662.157238.222673.7914
21.93381.640.76663.66771.2481.6279-0.01960.233-0.0426-0.1232-0.00910.19290.0360.23020.01550.26510.06370.00810.21580.02320.186244.626629.251551.7615
31.9538-0.1193-0.2223.13191.2781.40720.09070.1403-0.28260.0555-0.08510.17350.31670.0476-0.0730.24370.0263-0.01540.1408-0.01650.21143.778918.394652.9099
43.2976-2.53871.46614.617-2.28682.53360.00820.32210.0822-0.30760.12140.0081-0.17650.2341-0.09090.3004-0.064-0.0010.20250.0250.142334.235254.830743.9816
51.4430.1143-0.22891.1023-0.40782.0889-0.04170.02520.1474-0.04770.10520.2103-0.0344-0.377-0.07010.2610.0118-0.0110.22510.04770.239916.931650.815256.6444
62.7023-0.10670.40562.8333-1.03663.6395-0.11060.45290.2062-0.4160.1130.2635-0.2598-0.1652-0.0140.3618-0.053-0.05950.27510.11230.242220.821858.620337.8459
73.37342.5754-0.62994.5257-2.16123.62120.1849-0.43810.65920.6850.06750.3287-0.6749-0.3587-0.28070.41610.05880.01650.2882-0.07150.233128.27552.902674.2935
83.4948-0.29450.87854.4399-0.35793.115-0.153-0.2228-0.29670.49180.2345-0.03720.2142-0.06670.10630.2406-0.01640.05490.18060.0710.221728.916326.36674.2029
92.313-0.09260.15045.2088-2.4554.0089-0.1159-0.0426-0.506-0.25710.14180.07370.7244-0.2968-0.08090.3823-0.08740.06260.25760.03450.322521.279522.913368.5592
104.8276-0.21630.02341.49390.32152.6968-0.0549-0.575-0.51480.3505-0.0086-0.03140.339-0.43510.040.3228-0.03140.01370.17010.09170.224821.997831.055276.6676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:346)
2X-RAY DIFFRACTION2chain 'A' and (resseq 347:436)
3X-RAY DIFFRACTION3chain 'A' and (resseq 437:532)
4X-RAY DIFFRACTION4chain 'B' and (resseq 3:52)
5X-RAY DIFFRACTION5chain 'B' and (resseq 53:289)
6X-RAY DIFFRACTION6chain 'B' and (resseq 290:346)
7X-RAY DIFFRACTION7chain 'B' and (resseq 347:376)
8X-RAY DIFFRACTION8chain 'B' and (resseq 377:436)
9X-RAY DIFFRACTION9chain 'B' and (resseq 437:482)
10X-RAY DIFFRACTION10chain 'B' and (resseq 483:532)

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