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- PDB-1t8t: Crystal Structure of human 3-O-Sulfotransferase-3 with bound PAP -

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Basic information

Entry
Database: PDB / ID: 1t8t
TitleCrystal Structure of human 3-O-Sulfotransferase-3 with bound PAP
Componentsheparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1
KeywordsTRANSFERASE / alpha-beta motif / substrate-binding cleft
Function / homology
Function and homology information


[heparan sulfate]-glucosamine 3-sulfotransferase 3 / protein sulfation / [heparan sulfate]-glucosamine 3-sulfotransferase 3 activity / [heparan sulfate]-glucosamine 3-sulfotransferase 1 activity / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / heparan sulfate proteoglycan biosynthetic process / HS-GAG biosynthesis / glycosaminoglycan biosynthetic process / sulfotransferase activity / branching involved in ureteric bud morphogenesis ...[heparan sulfate]-glucosamine 3-sulfotransferase 3 / protein sulfation / [heparan sulfate]-glucosamine 3-sulfotransferase 3 activity / [heparan sulfate]-glucosamine 3-sulfotransferase 1 activity / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / heparan sulfate proteoglycan biosynthetic process / HS-GAG biosynthesis / glycosaminoglycan biosynthetic process / sulfotransferase activity / branching involved in ureteric bud morphogenesis / plasma membrane => GO:0005886 / Golgi membrane / membrane
Similarity search - Function
Heparan sulfate sulfotransferase / Sulfotransferase domain / Sulfotransferase domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-3'-5'-DIPHOSPHATE / CITRIC ACID / Heparan sulfate glucosamine 3-O-sulfotransferase 3B1 / Heparan sulfate glucosamine 3-O-sulfotransferase 3A1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMoon, A.F. / Edavettal, S.C. / Krahn, J.M. / Munoz, E.M. / Negishi, M. / Linhardt, R.J. / Liu, J. / Pedersen, L.C.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Structural analysis of the sulfotransferase (3-o-sulfotransferase isoform 3) involved in the biosynthesis of an entry receptor for herpes simplex virus 1
Authors: Moon, A.F. / Edavettal, S.C. / Krahn, J.M. / Munoz, E.M. / Negishi, M. / Linhardt, R.J. / Liu, J. / Pedersen, L.C.
History
DepositionMay 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). ...BIOMOLECULE: THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THE BIOLOGICAL UNIT IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1
B: heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1905
Polymers62,1442
Non-polymers1,0473
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-22 kcal/mol
Surface area23530 Å2
MethodPISA
2
A: heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1
B: heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1
hetero molecules

A: heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1
B: heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,38010
Polymers124,2874
Non-polymers2,0936
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area14660 Å2
ΔGint-60 kcal/mol
Surface area43060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.338, 155.394, 93.323
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-1608-

HOH

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Components

#1: Protein heparan sulfate D-glucosaminyl 3-O-sulfotransferase 3A1 / heparin-glucosamine 3-O-sulfotransferase / 3-OST-3


Mass: 31071.830 Da / Num. of mol.: 2 / Fragment: catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: h3-OST-3 / Plasmid: pGEX-4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus-RIL / References: UniProt: Q9Y662, UniProt: Q9Y663*PLUS
#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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 Å3/Da / Density % sol: 38.5 %
Crystal growTemperature: 297 K / Method: micro-seeding / pH: 5.5
Details: sodium citrate, ammonium acetate, PEG 4000, PAP, pH 5.5, micro-seeding, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 6, 2004 / Details: Osmic mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 49160 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.11 / Net I/σ(I): 23.1
Reflection shellHighest resolution: 1.85 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 4843 / Rsym value: 0.297 / % possible all: 99.1

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1S6T

1s6t
PDB Unreleased entry


Resolution: 1.85→50 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 540140.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2386 5 %RANDOM
Rwork0.206 ---
all0.207 47743 --
obs0.206 45357 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.1958 Å2 / ksol: 0.339245 e/Å3
Displacement parametersBiso mean: 29.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---6.21 Å20 Å2
3---6.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4341 0 67 442 4850
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 322 4.7 %
Rwork0.261 6545 -
obs--83.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4PAP2.PARAMPAP2.TOP
X-RAY DIFFRACTION5CIT.PARAMCIT.TOP

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