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- PDB-6ggy: Paenibacillus sp. YM1 laminaribiose phosphorylase with sulphate bound -

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Basic information

Entry
Database: PDB / ID: 6ggy
TitlePaenibacillus sp. YM1 laminaribiose phosphorylase with sulphate bound
ComponentsLaminaribiose phosphorylase
KeywordsHYDROLASE / laminaribiose phosphorylase / Glycosyl hydrolase 94 / disaccharide synthesis / CARBOHYDRATE
Function / homology
Function and homology information


laminaribiose phosphorylase / laminaribiose phosphorylase activity / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
Laminaribiose phosphorylase
Similarity search - Component
Biological speciesPaenibacillus sp. YM1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.95 Å
AuthorsKuhaudomlarp, S. / Walpole, S. / Stevenson, C.E.M. / Nepogodiev, S.A. / Lawson, D.M. / Angulo, J. / Field, R.A.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/P010660/1 United Kingdom
Engineering and Physical Sciences Research CouncilBB/M02903411 United Kingdom
CitationJournal: Chembiochem / Year: 2019
Title: Unravelling the Specificity of Laminaribiose Phosphorylase from Paenibacillus sp. YM-1 towards Donor Substrates Glucose/Mannose 1-Phosphate by Using X-ray Crystallography and Saturation ...Title: Unravelling the Specificity of Laminaribiose Phosphorylase from Paenibacillus sp. YM-1 towards Donor Substrates Glucose/Mannose 1-Phosphate by Using X-ray Crystallography and Saturation Transfer Difference NMR Spectroscopy.
Authors: Kuhaudomlarp, S. / Walpole, S. / Stevenson, C.E.M. / Nepogodiev, S.A. / Lawson, D.M. / Angulo, J. / Field, R.A.
History
DepositionMay 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Laminaribiose phosphorylase
B: Laminaribiose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,88220
Polymers203,7352
Non-polymers1,14718
Water16,069892
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, PISA
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10290 Å2
ΔGint-69 kcal/mol
Surface area57510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.704, 146.704, 222.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A4 - 907
2010B4 - 907

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Components

#1: Protein Laminaribiose phosphorylase /


Mass: 101867.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Two residues of sequence Gly-Pro are appended to the N-terminus of the native sequence which remain after tag cleavage
Source: (gene. exp.) Paenibacillus sp. YM1 (bacteria) / Gene: lbpA / Plasmid: pOPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D7UT17, laminaribiose phosphorylase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 892 / 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: 2.94 Å3/Da / Density % sol: 58.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Null

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.95→103.74 Å / Num. obs: 176355 / % possible obs: 100 % / Redundancy: 18.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.21 / Rpim(I) all: 0.05 / Rrim(I) all: 0.216 / Net I/σ(I): 13 / Num. measured all: 3267901 / Scaling rejects: 26
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.95-1.9818.81.91386400.6960.4481.966100
10.68-103.7415.10.03712660.9990.010.03999.9

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.95→103.74 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.512 / SU ML: 0.121 / SU R Cruickshank DPI: 0.1499 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.15 / ESU R Free: 0.133
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 8729 5 %RANDOM
Rwork0.2016 ---
obs0.2027 167499 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 101.98 Å2 / Biso mean: 37.577 Å2 / Biso min: 6.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2--0.59 Å20 Å2
3----1.17 Å2
Refinement stepCycle: final / Resolution: 1.95→103.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13945 0 64 937 14946
Biso mean--40.49 32.18 -
Num. residues----1813
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914452
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212894
X-RAY DIFFRACTIONr_angle_refined_deg1.41.94519627
X-RAY DIFFRACTIONr_angle_other_deg0.958329688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.28251837
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.28123.439692
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.454152199
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.68815112
X-RAY DIFFRACTIONr_chiral_restr0.0830.22097
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216635
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023213
Refine LS restraints NCS

Ens-ID: 1 / Number: 60008 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.95→2.001 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 650 -
Rwork0.309 12190 -
all-12840 -
obs--99.84 %
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)
10.6582-0.1725-0.17480.49680.31782.3105-0.2230.1399-0.15220.1868-0.09430.0720.885-0.41990.31730.4863-0.26390.19720.1652-0.10590.089150.0825-1.4553.8155
21.8377-1.4390.51671.1508-0.4461.4626-0.34680.07180.10850.3365-0.0849-0.03320.0246-1.09470.43160.2565-0.31660.19531.1678-0.52970.305828.476517.382939.2661
30.6686-0.06910.12251.02650.11481.72620.0210.02050.0658-0.0021-0.3940.36210.059-0.91770.3730.0677-0.07460.03640.6984-0.32920.208830.267918.407622.7112
42.6754-0.893-0.91472.69061.88691.3720.17630.20170.2532-0.2541-0.48390.5776-0.1204-0.41320.30750.6445-0.54320.02161.0874-0.27910.54918.9522-8.721416.2414
50.8378-0.0122-0.2650.63430.39141.853-0.0658-0.0208-0.01960.07730.0249-0.04880.12020.27890.04090.0712-0.0220.01450.09080.00340.012973.696522.437550.8866
64.839-0.0334-1.05832.0893-0.34181.95530.10160.45130.1137-0.18280.11660.1429-0.3695-0.193-0.21820.29390.0480.05320.07790.04480.064951.875749.266568.1486
71.1253-0.1908-0.78910.8649-0.01241.73720.0936-0.09060.18870.1270.0289-0.0133-0.35380.0659-0.12250.216-0.0220.02380.0621-0.01480.032755.086840.704183.4995
83.162-2.17963.0086.2257-2.13972.8938-0.3915-0.05120.18730.40470.3351-0.2513-0.39880.0720.05630.4896-0.3506-0.03060.7313-0.18810.490682.877753.288786.3433
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 359
2X-RAY DIFFRACTION2A360 - 430
3X-RAY DIFFRACTION3A431 - 872
4X-RAY DIFFRACTION4A873 - 911
5X-RAY DIFFRACTION5B4 - 370
6X-RAY DIFFRACTION6B371 - 482
7X-RAY DIFFRACTION7B483 - 865
8X-RAY DIFFRACTION8B866 - 908

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