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- PDB-3sqm: Crystal Structure of Glycoside Hydrolase from Synechococcus Compl... -

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Basic information

Entry
Database: PDB / ID: 3sqm
TitleCrystal Structure of Glycoside Hydrolase from Synechococcus Complexed with N-acetyl-D-glucosamine
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 / peptidoglycan turnover / hydrolase activity, hydrolyzing O-glycosyl compounds / transferase activity / 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: 2.703 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 Complexed with N-acetyl-D-glucosamine
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 1.1Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycosyl hydrolase family 3
B: Glycosyl hydrolase family 3
C: Glycosyl hydrolase family 3
D: Glycosyl hydrolase family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,54924
Polymers234,4294
Non-polymers2,12020
Water3,801211
1
A: Glycosyl hydrolase family 3
B: Glycosyl hydrolase family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,18711
Polymers117,2152
Non-polymers9739
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7520 Å2
ΔGint-14 kcal/mol
Surface area34540 Å2
MethodPISA
2
C: Glycosyl hydrolase family 3
D: Glycosyl hydrolase family 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,36213
Polymers117,2152
Non-polymers1,14711
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7970 Å2
ΔGint-33 kcal/mol
Surface area35190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.139, 125.139, 233.745
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-543-

ACY

21B-543-

ACY

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Components

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Glycosyl hydrolase family 3


Mass: 58607.250 Da / Num. of mol.: 4
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
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 227 molecules

#3: Chemical
ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H4O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 211 / 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: 2.25 Å3/Da / Density % sol: 45.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 0.1M ammonium acetate 0.1M BIS-TRIS pH 6.8, 23.3% PEG 3350, 5.3mM N-ACETYL-D-GLUCOSAMINE, 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: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2011 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 58559 / Num. obs: 58559 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 40.52 Å2 / Rsym value: 0.061 / Net I/σ(I): 8.9
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 2841 / Rsym value: 0.635 / % possible all: 99.3

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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: 2.703→40.961 Å / SU ML: 0.66 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24.29 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2548 5.05 %random
Rwork0.159 ---
all0.163 50442 --
obs0.163 50442 85.89 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.501 Å2 / ksol: 0.295 e/Å3
Displacement parametersBiso mean: 45.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.6212 Å2-0 Å2-0 Å2
2--2.6212 Å20 Å2
3----5.2424 Å2
Refinement stepCycle: LAST / Resolution: 2.703→40.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15893 0 140 211 16244
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916471
X-RAY DIFFRACTIONf_angle_d1.3922486
X-RAY DIFFRACTIONf_dihedral_angle_d15.6765991
X-RAY DIFFRACTIONf_chiral_restr0.0932599
X-RAY DIFFRACTIONf_plane_restr0.0072911
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.7026-2.75460.4177610.26051007106834
2.7546-2.81080.3433750.23481204127940
2.8108-2.87190.3583800.2151454153448
2.8719-2.93870.2987860.22651768185458
2.9387-3.01220.3511260.222283240975
3.0122-3.09360.28711420.22342897303994
3.0936-3.18460.29911500.21573045319599
3.1846-3.28730.29821600.194530833243100
3.2873-3.40480.27761600.194930503210100
3.4048-3.5410.25971520.168330913243100
3.541-3.70210.25041940.159530343228100
3.7021-3.89710.21481840.140730933277100
3.8971-4.14110.18071650.127530783243100
4.1411-4.46040.19121680.116431033271100
4.4604-4.90860.18731540.112431283282100
4.9086-5.61740.19491550.145331533308100
5.6174-7.07140.18521720.154131553327100
7.0714-40.9660.19891640.14993268343298
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)
10.55830.28420.57621.05340.89481.0985-0.180.08920.1811-0.34280.12850.0165-0.46990.08850.12990.17350.1037-0.28490.128-0.089-0.025667.8406-43.406741.1773
23.67512.2797-0.40943.0057-2.40475.8865-0.03890.72690.0466-0.31650.43390.3538-0.2883-0.8857-0.23970.44810.1229-0.19690.2735-0.04040.27959.9111-55.697220.3395
31.2069-0.72670.06111.3140.35151.66320.01790.33520.0506-0.3632-0.0636-0.1799-0.4030.5627-0.10110.3328-0.21080.05150.4737-0.10830.130785.7402-58.558616.4213
40.4332-0.2009-0.08620.76560.06071.00620.09740.1227-0.0787-0.16630.02630.16570.2363-0.0737-0.01450.11960.0863-0.20090.1142-0.03220.099867.3462-91.115627.2016
53.13662.80612.72724.68153.32194.2090.1707-0.4149-0.16020.1304-0.08170.53340.2901-0.6680.08990.193-0.0118-0.05050.2640.12940.358654.4904-89.992632.5225
61.76571.0616-0.64481.8111-0.47141.37540.0609-0.06540.01570.11210.0386-0.2707-0.16810.4307-0.04490.0891-0.02210.00310.323-0.09350.122888.9401-71.568341.3314
72.462-0.1382-0.21860.86870.35371.48350.02540.078-0.0133-0.07020.1222-0.2975-0.04370.7267-0.13740.14280.05890.00660.4638-0.08750.18193.7788-76.303837.6283
83.41291.2452-1.18571.4896-0.52861.6152-0.18930.1401-0.259-0.1220.1345-0.08780.39370.08270.0280.185-0.00540.03160.086-0.00160.054248.1012-10.715122.2362
90.99140.0273-0.54130.8186-0.08611.2983-0.01460.18170.11-0.12570.08970.055-0.0504-0.2144-0.03120.1306-0.0430.03590.04050.01650.028140.7631.64968.722
103.97620.6437-2.87630.199-0.55262.1624-0.40360.3925-0.4903-0.18660.09020.03290.4929-0.20950.47590.2156-0.0980.03540.1795-0.05290.165840.1896-14.270910.3442
111.6290.9248-0.3341.8924-0.22661.0350.12240.10930.2507-0.03020.0557-0.1416-0.28290.1133-0.00430.2641-0.08560.1510.12230.00350.165367.100612.9186-4.4626
121.9225-0.10930.25732.3919-0.28151.626-0.12860.38080.3724-0.10760.2201-0.1229-0.32380.0181-0.04110.2481-0.07240.07250.12750.00960.173663.048912.6393-8.8726
130.8277-0.4547-0.82710.80.31791.0619-0.149-0.44960.0020.22360.2371-0.27790.26080.5178-0.02350.25560.17940.05710.2693-0.01990.110588.541-17.65055.7074
140.5317-0.6472-0.27552.28670.32341.1844-0.1805-0.5310.11130.50070.4307-0.20890.11430.42-0.04280.28440.04950.04350.5532-0.08630.194174.85850.50726.0401
153.60350.621-1.87755.48470.93634.15290.01450.140.0491-0.04830.21050.118-0.08490.0954-0.09850.1129-0.0386-0.0280.1427-0.03840.090772.01419.136615.8218
160.15650.2393-0.31751.78150.24341.02730.1202-0.27290.27940.02930.2249-0.2275-0.38340.6675-0.27740.3296-0.14670.09490.5774-0.22630.308381.635911.682719.6819
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:348)
2X-RAY DIFFRACTION2chain 'A' and (resseq 349:376)
3X-RAY DIFFRACTION3chain 'A' and (resseq 377:532)
4X-RAY DIFFRACTION4chain 'B' and (resseq 6:328)
5X-RAY DIFFRACTION5chain 'B' and (resseq 329:362)
6X-RAY DIFFRACTION6chain 'B' and (resseq 363:436)
7X-RAY DIFFRACTION7chain 'B' and (resseq 437:532)
8X-RAY DIFFRACTION8chain 'C' and (resseq 1:52)
9X-RAY DIFFRACTION9chain 'C' and (resseq 53:328)
10X-RAY DIFFRACTION10chain 'C' and (resseq 329:362)
11X-RAY DIFFRACTION11chain 'C' and (resseq 363:482)
12X-RAY DIFFRACTION12chain 'C' and (resseq 483:532)
13X-RAY DIFFRACTION13chain 'D' and (resseq 4:348)
14X-RAY DIFFRACTION14chain 'D' and (resseq 349:400)
15X-RAY DIFFRACTION15chain 'D' and (resseq 401:434)
16X-RAY DIFFRACTION16chain 'D' and (resseq 435:532)

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