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- PDB-5t03: Crystal structure of heparan sulfate 6-O-sulfotransferase with bo... -

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Basic information

Entry
Database: PDB / ID: 5t03
TitleCrystal structure of heparan sulfate 6-O-sulfotransferase with bound PAP and glucuronic acid containing hexasaccharide substrate
Componentsmaltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein
KeywordsTRANSFERASE / heparan sulfate / sulfotransferase / complex
Function / homologyBacterial extracellular solute-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Sulfotransferase family / P-loop containing nucleoside triphosphate hydrolase / Sulfotransferase / Heparan sulphate 6-sulfotransferase/Protein-tyrosine sulfotransferase / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / heparan sulfate 6-O-sulfotransferase activity ...Bacterial extracellular solute-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Sulfotransferase family / P-loop containing nucleoside triphosphate hydrolase / Sulfotransferase / Heparan sulphate 6-sulfotransferase/Protein-tyrosine sulfotransferase / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / heparan sulfate 6-O-sulfotransferase activity / 3'-phosphoadenosine 5'-phosphosulfate binding / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / Transferases, Transferring sulfur-containing groups, Sulfotransferases / sulfotransferase activity / oligosaccharide binding / carbohydrate transmembrane transporter activity / periplasmic space / integral component of membrane / Heparan-sulfate 6-O-sulfotransferase 3-B / Maltose/maltodextrin-binding periplasmic protein
Function and homology information
Specimen sourceEscherichia coli O157:H7 (bacteria)
Danio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 2.1 Å resolution
AuthorsPedersen, L.C. / Moon, A.F. / Krahn, J.M. / Liu, J.
Funding supportUnited States , 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesGM102137United States
National Institutes of Health/National Heart, Lung, and Blood InstituteHL094463United States
CitationJournal: ACS Chem. Biol. / Year: 2017
Title: Structure Based Substrate Specificity Analysis of Heparan Sulfate 6-O-Sulfotransferases.
Authors: Xu, Y. / Moon, A.F. / Xu, S. / Krahn, J.M. / Liu, J. / Pedersen, L.C.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 15, 2016 / Release: Feb 1, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Feb 1, 2017Structure modelrepositoryInitial release
1.1Sep 20, 2017Structure modelAuthor supporting evidencepdbx_audit_support_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: maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein
B: maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,31757
Polyers157,1142
Non-polymers7,20355
Water16,484915
1
A: maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,38533
Polyers78,5571
Non-polymers3,82832
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,93224
Polyers78,5571
Non-polymers3,37423
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)75.778, 128.396, 179.722
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

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Protein/peptide , 1 types, 2 molecules AB

#1: Protein/peptide maltose binding protein - heparan sulfate 6-O-sulfotransferase isoform 3 fusion protein / MBP / MMBP / Maltodextrin-binding protein / HS 6-OST-3


Mass: 78557.203 Da / Num. of mol.: 2
Details: This is an N-terminal MBP fusion to HS 6-O-sulfotransferase from zebrafish isoform 3. To keep the ...This is an N-terminal MBP fusion to HS 6-O-sulfotransferase from zebrafish isoform 3. To keep the correct numbering with the 6-O-sulfotransferase add 1000.
Mutation: D82A, K83A, E172A, N173A, K239A, E359A, K362A, D363A
Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Danio rerio (zebrafish)
Gene: malE, Z5632, ECs5017, hs6st3 / Production host: Escherichia coli (E. coli)
References: UniProt: P0AEY0, UniProt: A0MGZ7, Transferases, Transferring sulfur-containing groups, Sulfotransferases

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Non-polymers , 10 types, 970 molecules

#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Formula: C10H15N5O10P2 / Adenosine 3',5'-bisphosphate
#3: Chemical
ChemComp-GNS / N-SULFO-ALPHA-D-GLUCOSAMINE


Mass: 259.234 Da / Num. of mol.: 6 / Formula: C6H13NO8S
#4: Chemical
ChemComp-BDP / BETA-D-GLUCOPYRANURONIC ACID / D-GLUCURONIC ACID


Mass: 194.139 Da / Num. of mol.: 6 / Formula: C6H10O7 / Glucuronic acid
#5: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 2 / Formula: C6H5NO3 / 4-Nitrophenol
#6: Chemical
ChemComp-GLC / ALPHA-D-GLUCOSE


Mass: 180.156 Da / Num. of mol.: 8 / Formula: C6H12O6 / Glucose
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Formula: C2H6O2 / Ethylene glycol
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Formula: Cl / Chloride
#9: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Formula: Na / Sodium
#10: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 4 / Formula: C4H6O6
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 915 / Formula: H2O / Water

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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: 2.78 / Density percent sol: 55.79 %
Crystal growTemp: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Tris pH 7.5, 200mM di-sodium tartrate, 18-19% PEG 3350

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Collection date: Mar 11, 2016
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionD resolution high: 2.1 Å / D resolution low: 5 Å / Number obs: 102512 / NetI over sigmaI: 6.3 / Redundancy: 6 % / Percent possible obs: 99.7

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefineMethod to determine structure: MOLECULAR REPLACEMENT / Overall SU ML: 0.19 / Cross valid method: THROUGHOUT / Sigma F: 1.36 / Overall phase error: 20.88 / Stereochemistry target values: ML
Solvent computationSolvent shrinkage radii: 0.9 Å / Solvent vdw probe radii: 1.11 Å / Solvent model details: FLAT BULK SOLVENT MODEL
Least-squares processR factor R free: 0.2117 / R factor R work: 0.1735 / R factor obs: 0.1744 / Highest resolution: 2.1 Å / Lowest resolution: 38.648 Å / Number reflection R free: 2273 / Number reflection obs: 102388 / Percent reflection R free: 2.22 / Percent reflection obs: 99.5
Refine hist #LASTHighest resolution: 2.1 Å / Lowest resolution: 38.648 Å
Number of atoms included #LASTProtein: 10463 / Nucleic acid: 0 / Ligand: 441 / Solvent: 915 / Total: 11819
Refine LS restraints
Refine IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611256
X-RAY DIFFRACTIONf_angle_d0.78715333
X-RAY DIFFRACTIONf_dihedral_angle_d11.5226560
X-RAY DIFFRACTIONf_chiral_restr0.0491718
X-RAY DIFFRACTIONf_plane_restr0.0051938
Refine LS shell

Refine ID: X-RAY DIFFRACTION

Highest resolutionR factor R freeR factor R workLowest resolutionNumber reflection R freeNumber reflection R workPercent reflection obs
2.10010.26800.21022.1458134586695.00
2.14580.26570.19422.1957139615399.00
2.19570.22650.19012.2506142616599.00
2.25060.24480.18852.31151406215100.00
2.31150.22610.18742.37951396211100.00
2.37950.25830.18782.45621446246100.00
2.45620.23890.18692.54401406219100.00
2.54400.25360.18112.64591426242100.00
2.64590.23030.18652.76621386269100.00
2.76620.24660.19102.91201466296100.00
2.91200.25810.19323.09441426222100.00
3.09440.21390.18443.33321446309100.00
3.33320.20320.16853.66841446336100.00
3.66840.16440.14694.19871446334100.00
4.19870.18530.14605.28781466404100.00
5.28780.18270.174938.65431496628100.00
Refine TLS

Method: refined / Refine ID: X-RAY DIFFRACTION

IDL11L12L13L22L23L33S11S12S13S21S22S23S31S32S33T11T12T13T22T23T33Origin xOrigin yOrigin z
10.2867-0.3896-0.28570.48360.22720.59700.03600.3315-0.0601-0.1775-0.08220.3622-0.1283-0.17440.00000.32430.0071-0.00300.3093-0.04330.38169.4067-23.9993-26.5891
20.2977-0.08240.07430.12660.16590.2581-0.1530-0.2000-0.09970.46360.13250.43430.0139-0.0638-0.03160.45760.04290.16830.31750.02050.37586.1563-20.9122-9.8344
30.38080.38330.24760.91850.05200.47990.0431-0.0695-0.02000.21900.0215-0.15490.10780.1074-0.00000.32040.0583-0.02860.2542-0.02260.201536.2301-18.3445-12.7753
41.0328-0.09690.11311.15550.24490.6619-0.0666-0.0050-0.07740.24130.05950.09410.14410.0858-0.00000.32010.03920.02690.18690.00900.188725.7403-23.4930-15.6165
50.00690.0004-0.00360.01500.01010.02850.0961-0.3176-0.15970.25270.14850.1326-0.1033-0.11300.00000.51900.04510.01510.35210.03090.266727.6900-23.6948-3.9002
60.3025-0.25100.04140.19010.00360.0813-0.06930.04240.21420.16640.0233-0.06840.00260.0698-0.00000.3191-0.00180.00440.2610-0.00540.351324.27942.6257-16.3929
70.6900-0.24260.17450.40830.19720.75910.07330.19950.3267-0.1116-0.0671-0.0885-0.3746-0.15640.00380.26390.06670.05800.20540.06790.27191.305330.1448-32.3827
81.5483-0.1977-0.07320.78350.06050.52090.05050.3656-0.1703-0.05910.0090-0.0277-0.0258-0.08430.05870.12570.01990.02090.2496-0.01190.17104.19509.3039-37.3384
90.85810.08070.20110.18220.12610.71850.0609-0.1405-0.11170.17610.0037-0.05530.0024-0.16400.00000.20960.03270.02290.22930.02910.23581.308015.8372-19.7167
100.4970-0.33520.07640.4198-0.43840.41870.0230-0.0831-0.11330.35020.0463-0.0700-0.0029-0.00430.00390.19430.0109-0.00240.18570.03010.166112.456219.4268-13.5234
111.14700.26690.40070.26580.02670.77200.38370.0642-0.35590.2464-0.0754-0.36540.56660.23830.13340.5761-0.0316-0.21400.2944-0.01460.410324.280610.633015.1349
121.0797-0.20300.16990.98230.13890.66170.3830-0.2928-0.25410.3875-0.19250.15750.5890-0.71960.31660.5972-0.3365-0.06480.59550.07320.2515-3.54658.69739.9761
130.6819-0.30120.31920.88310.56371.08510.20640.13800.12350.1551-0.0932-0.27320.27990.00320.02630.4597-0.0878-0.08000.33810.03980.300617.253517.458912.3061
140.54340.03030.02470.14220.17260.42990.2846-0.1905-0.18370.2559-0.2437-0.21210.3220-0.20390.00560.6921-0.2283-0.13780.45120.09370.38645.333310.479016.9449
150.1075-0.19150.07850.65590.26290.6907-0.30830.46830.1546-0.65170.4183-0.4450-0.35080.41650.12070.5451-0.1629-0.01420.42360.04870.44317.4884-10.869831.4918
160.48200.0306-0.14470.5838-0.14350.6544-0.0142-0.0384-0.13220.00540.0103-0.04580.2423-0.0502-0.00000.2160-0.0128-0.01000.16150.02490.2488-1.8661-30.907248.8444
170.99130.27920.23480.75210.08090.48830.0064-0.05340.05030.09190.0058-0.01040.0579-0.0303-0.00000.1105-0.0001-0.00630.15330.01730.1488-1.4147-10.892257.3136
180.28280.1411-0.21430.24840.27430.4903-0.05940.20790.1283-0.08210.0857-0.0627-0.0609-0.0715-0.00000.1724-0.0208-0.02320.22800.01410.2210-3.5052-15.920938.1908
190.52920.25190.04990.3710-0.31480.5882-0.12940.15500.0397-0.12890.05390.0143-0.0802-0.0352-0.08220.1617-0.05570.01110.23050.01450.21306.1111-12.120037.1072
200.0270-0.01980.00430.00150.0026-0.00740.69520.3015-0.03960.1775-0.05280.00730.17560.62800.00000.7271-0.11750.15700.8029-0.19780.718317.6864-29.06108.1492
Refine TLS group
IDRefine IDRefine TLS IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:66)
2X-RAY DIFFRACTION2(chain A and resid 67:107)
3X-RAY DIFFRACTION3(chain A and resid 108:175)
4X-RAY DIFFRACTION4(chain A and resid 176:320)
5X-RAY DIFFRACTION5(chain A and resid 321:327)
6X-RAY DIFFRACTION6(chain A and resid 328:1087)
7X-RAY DIFFRACTION7(chain A and resid 1088:1169)
8X-RAY DIFFRACTION8(chain A and resid 1170:1291)
9X-RAY DIFFRACTION9(chain A and resid 1292:1345)
10X-RAY DIFFRACTION10(chain A and resid 1346:1383)
11X-RAY DIFFRACTION11(chain B and resid 2:111)
12X-RAY DIFFRACTION12(chain B and resid 112:243)
13X-RAY DIFFRACTION13(chain B and resid 244:307)
14X-RAY DIFFRACTION14(chain B and resid 308:355)
15X-RAY DIFFRACTION15(chain B and resid 356:1086)
16X-RAY DIFFRACTION16(chain B and resid 1087:1170)
17X-RAY DIFFRACTION17(chain B and resid 1171:1290)
18X-RAY DIFFRACTION18(chain B and resid 1291:1344)
19X-RAY DIFFRACTION19(chain B and resid 1345:1373)
20X-RAY DIFFRACTION20(chain B and resid 1374:1390)

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