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- PDB-6b6l: The crystal structure of glycosyl hydrolase family 2 (GH2) member... -

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Basic information

Entry
Database: PDB / ID: 6b6l
TitleThe crystal structure of glycosyl hydrolase family 2 (GH2) member from Bacteroides cellulosilyticus DSM 14838
ComponentsGlycosyl hydrolase family 2, sugar binding domain protein
KeywordsHYDROLASE / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomics / MCSG / glycosyl hydrolase
Function / homology
Function and homology information


carbohydrate catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds
Similarity search - Function
Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich ...Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Glycosyl hydrolase family 2, sugar binding domain protein
Similarity search - Component
Biological speciesBacteroides cellulosilyticus DSM 14838 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsTan, K. / Joachimiak, G. / Nocek, B. / Enddres, M. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM115586 United States
CitationJournal: To Be Published
Title: The crystal structure of glycosyl hydrolase family 2 (GH2) member from Bacteroides cellulosilyticus DSM 14838
Authors: Tan, K. / Joachimiak, G. / Nocek, B. / Enddres, M. / Babnigg, G. / Joachimiak, A.
History
DepositionOct 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase family 2, sugar binding domain protein
B: Glycosyl hydrolase family 2, sugar binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,7128
Polymers175,3882
Non-polymers3246
Water13,097727
1
A: Glycosyl hydrolase family 2, sugar binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,9105
Polymers87,6941
Non-polymers2164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycosyl hydrolase family 2, sugar binding domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,8023
Polymers87,6941
Non-polymers1082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.528, 227.135, 66.902
Angle α, β, γ (deg.)90.00, 108.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Glycosyl hydrolase family 2, sugar binding domain protein


Mass: 87693.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides cellulosilyticus DSM 14838 (bacteria)
Gene: BACCELL_00063 / Plasmid: pMCSG73 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Gold(DE3) / References: UniProt: E2N721
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 727 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.2M Potassium Chloride 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 7, 2015 / Details: mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2→48.88 Å / Num. obs: 110119 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 23.77 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.051 / Rrim(I) all: 0.099 / Χ2: 0.85 / Net I/σ(I): 15.4
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.689 / Mean I/σ(I) obs: 1.67 / Num. unique obs: 5534 / CC1/2: 0.52 / Rpim(I) all: 0.508 / Rrim(I) all: 0.86 / Χ2: 0.805 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2→34.881 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.85
RfactorNum. reflection% reflectionSelection details
Rfree0.2082 5319 4.95 %random
Rwork0.1628 ---
obs0.165 107510 96.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→34.881 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11439 0 21 727 12187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01411737
X-RAY DIFFRACTIONf_angle_d1.23415942
X-RAY DIFFRACTIONf_dihedral_angle_d13.4026895
X-RAY DIFFRACTIONf_chiral_restr0.0791762
X-RAY DIFFRACTIONf_plane_restr0.0082059
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9858-2.00840.3137820.23191588X-RAY DIFFRACTION46
2.0084-2.0320.26551390.232688X-RAY DIFFRACTION76
2.032-2.05680.30011560.21643128X-RAY DIFFRACTION87
2.0568-2.08280.27381700.20183304X-RAY DIFFRACTION95
2.0828-2.11020.24081880.19743417X-RAY DIFFRACTION98
2.1102-2.13910.25861850.19243518X-RAY DIFFRACTION99
2.1391-2.16970.28171800.18563485X-RAY DIFFRACTION99
2.1697-2.20210.21231670.17693565X-RAY DIFFRACTION100
2.2021-2.23650.25331560.1733515X-RAY DIFFRACTION100
2.2365-2.27310.24741790.1783541X-RAY DIFFRACTION100
2.2731-2.31230.22851750.17383558X-RAY DIFFRACTION100
2.3123-2.35440.24441720.17073490X-RAY DIFFRACTION100
2.3544-2.39960.22751760.16823546X-RAY DIFFRACTION100
2.3996-2.44860.21232120.16873465X-RAY DIFFRACTION100
2.4486-2.50180.21532060.16933566X-RAY DIFFRACTION100
2.5018-2.560.21652060.16753429X-RAY DIFFRACTION100
2.56-2.6240.21681720.16613564X-RAY DIFFRACTION100
2.624-2.69490.2292030.17173506X-RAY DIFFRACTION100
2.6949-2.77420.24111870.17483506X-RAY DIFFRACTION100
2.7742-2.86370.22661910.17963519X-RAY DIFFRACTION100
2.8637-2.9660.23191970.17963526X-RAY DIFFRACTION100
2.966-3.08470.23342120.17553460X-RAY DIFFRACTION100
3.0847-3.2250.19912010.1723529X-RAY DIFFRACTION100
3.225-3.39490.22231720.17493565X-RAY DIFFRACTION100
3.3949-3.60740.19531570.15643543X-RAY DIFFRACTION100
3.6074-3.88560.17311760.14363541X-RAY DIFFRACTION100
3.8856-4.2760.16531800.1363529X-RAY DIFFRACTION100
4.276-4.89330.15781730.12243534X-RAY DIFFRACTION99
4.8933-6.15950.15821700.14073545X-RAY DIFFRACTION100
6.1595-34.88670.17861790.15183521X-RAY DIFFRACTION98
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)
11.72660.4018-0.12721.36250.19181.3666-0.1093-0.5267-0.52430.0301-0.0546-0.19880.41620.1275-0.01930.1810.06810.08020.26240.18470.23815.83-14.566532.5865
20.92930.1535-0.29810.4412-0.11691.4743-0.0224-0.15150.0541-0.0164-0.01630.0672-0.0042-0.01870.02780.0856-0.0114-0.01080.1398-0.02150.1071-2.717.93319.3287
30.81490.5866-0.04592.0997-0.3431.61530.00720.08580.2254-0.56670.09150.0862-0.4944-0.0334-0.05820.4861-0.0144-0.01640.15220.05330.332314.05274.67434.4102
41.1095-0.1164-0.02091.24630.17250.92360.041-0.18220.07950.08710.008-0.0365-0.07680.083-0.0490.2053-0.02020.00360.16110.01190.241415.290758.144426.3624
51.15060.2270.69622.07411.51331.37650.00770.0354-0.0702-0.21460.133-0.2128-0.05920.0444-0.14910.1936-0.0273-0.00260.13290.0130.244122.16738.49249.7802
61.28920.32690.26991.92230.66221.2743-0.04730.11560.079-0.3360.1110.1467-0.1059-0.0531-0.07030.2254-0.0638-0.04990.1610.04120.23213.133135.8916-3.0141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 26 through 275 )
2X-RAY DIFFRACTION2chain 'A' and (resid 276 through 797 )
3X-RAY DIFFRACTION3chain 'B' and (resid 26 through 179 )
4X-RAY DIFFRACTION4chain 'B' and (resid 180 through 515 )
5X-RAY DIFFRACTION5chain 'B' and (resid 516 through 606 )
6X-RAY DIFFRACTION6chain 'B' and (resid 607 through 797 )

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