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- PDB-1zrh: Crystal structure of Human heparan sulfate glucosamine 3-O-sulfot... -

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Basic information

Entry
Database: PDB / ID: 1zrh
TitleCrystal structure of Human heparan sulfate glucosamine 3-O-sulfotransferase 1 in complex with PAP
ComponentsHeparan sulfate glucosamine 3-O-sulfotransferase 1
KeywordsTRANSFERASE / SGC / Sulfotransferase HS3ST1 / Structural Genomics / Structural Genomics Consortium
Function / homology
Function and homology information


[heparan sulfate]-glucosamine 3-sulfotransferase 1 / [heparan sulfate]-glucosamine 3-sulfotransferase 1 activity / heparan sulfate proteoglycan biosynthetic process, enzymatic modification / HS-GAG biosynthesis / glycosaminoglycan biosynthetic process / sulfotransferase activity / Golgi lumen
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 / Heparan sulfate glucosamine 3-O-sulfotransferase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDong, A. / Dombrovski, L. / Loppnau, P. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of Human heparan sulfate glucosamine 3-O-sulfotransferase 1 in complex with PAP
Authors: Dong, A. / Dombrovski, L. / Loppnau, P. / Sundstrom, M. / Arrowsmith, C.H. / Edwards, A.M. / Bochkarev, A. / Plotnikov, A.N.
History
DepositionMay 19, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heparan sulfate glucosamine 3-O-sulfotransferase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7612
Polymers32,3341
Non-polymers4271
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.887, 135.255, 48.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212

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Components

#1: Protein Heparan sulfate glucosamine 3-O-sulfotransferase 1 / E.C.2.8.2.23 / Sulfotransferase HS3ST1 / Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 1 / Heparan sulfate 3- ...Sulfotransferase HS3ST1 / Heparan sulfate D-glucosaminyl 3-O-sulfotransferase 1 / Heparan sulfate 3-O-sulfotransferase 1 / h3-OST-1


Mass: 32333.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HS3ST1, 3OST, 3OST1 / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O14792, [heparan sulfate]-glucosamine 3-sulfotransferase 1
#2: Chemical ChemComp-A3P / ADENOSINE-3'-5'-DIPHOSPHATE


Type: RNA linking / Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O
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: 3 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 4.6
Details: 2.0 - 2.4 M Sodium Formate, 0.1 M Sodium-Acetate pH 4.6, 5% Glycerol, VAPOR DIFFUSION, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 16, 2005 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→67.57 Å / Num. all: 22876 / Num. obs: 22876 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.114 / Rsym value: 0.114 / Net I/σ(I): 8.5
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 3.04 / Num. unique all: 2235 / Rsym value: 0.551 / % possible all: 98.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SCALEPACKdata scaling
PHASESphasing
REFMAC5.2refinement
CrystalClear(MSC/RIGAKU)data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VKJ

1vkj


Resolution: 2.1→67.57 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.715 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.173 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20911 741 3.2 %RANDOM
Rwork0.18408 ---
all0.1849 22105 --
obs0.1849 22105 98.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.827 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.87 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 2.1→67.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2207 0 27 177 2411
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0212310
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.9543138
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9145262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.08922.727121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.83915381
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8381519
X-RAY DIFFRACTIONr_chiral_restr0.1240.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021799
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1970.21063
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21501
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2171
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.241
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4420.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2121.51373
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85722147
X-RAY DIFFRACTIONr_scbond_it2.91531100
X-RAY DIFFRACTIONr_scangle_it4.3174.5991
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 52 -
Rwork0.239 1564 -
obs--97.47 %

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