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- PDB-1p49: Structure of Human Placental Estrone/DHEA Sulfatase -

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Basic information

Entry
Database: PDB / ID: 1p49
TitleStructure of Human Placental Estrone/DHEA Sulfatase
ComponentsSTERYL-SULFATASE
KeywordsHYDROLASE / steroid biosynthesis / steroid sulfatase / estrone sulfate / dehydroepiandrosterone sulfate / human placental enzyme / endoplasmic reticulum membrane-bound
Function / homology
Function and homology information


steryl-sulfatase / steryl-sulfatase activity / Metabolism of steroid hormones / The activation of arylsulfatases / arylsulfatase activity / sulfuric ester hydrolase activity / Glycosphingolipid catabolism / steroid catabolic process / epidermis development / female pregnancy ...steryl-sulfatase / steryl-sulfatase activity / Metabolism of steroid hormones / The activation of arylsulfatases / arylsulfatase activity / sulfuric ester hydrolase activity / Glycosphingolipid catabolism / steroid catabolic process / epidermis development / female pregnancy / lysosome / endosome / endoplasmic reticulum lumen / intracellular membrane-bounded organelle / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / membrane / metal ion binding / plasma membrane
Similarity search - Function
Helix hairpin bin / C-terminal region of aryl-sulfatase / Arylsulfatase, C-terminal domain - #10 / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Arylsulfatase, C-terminal domain / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A ...Helix hairpin bin / C-terminal region of aryl-sulfatase / Arylsulfatase, C-terminal domain - #10 / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Arylsulfatase, C-terminal domain / Sulfatase, N-terminal / Sulfatase / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Helix Hairpins / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Steryl-sulfatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 2.6 Å
AuthorsHernandez-Guzman, F.G. / Higashiyama, T. / Pangborn, W. / Osawa, Y. / Ghosh, D.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structure of Human Estrone Sulfatase Suggests Functional Roles of Membrane Association
Authors: Hernandez-Guzman, F.G. / Higashiyama, T. / Pangborn, W. / Osawa, Y. / Ghosh, D.
History
DepositionApr 21, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Dec 2, 2015Group: Non-polymer description
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 600HETEROGEN 2-AMINO-3-OXO-4-SULFO-BUTYRIC ACID, ALS75, is a post-translationally modified Cys75. ALS ...HETEROGEN 2-AMINO-3-OXO-4-SULFO-BUTYRIC ACID, ALS75, is a post-translationally modified Cys75. ALS Is referred to as hydroxyformylglycine (FGS75) in the related publication.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STERYL-SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2147
Polymers63,0521
Non-polymers1,1626
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: STERYL-SULFATASE
hetero molecules

A: STERYL-SULFATASE
hetero molecules

A: STERYL-SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,64221
Polymers189,1553
Non-polymers3,48718
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area9040 Å2
ΔGint-58 kcal/mol
Surface area62970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.980, 116.980, 102.660
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-606-

PO4

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Components

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Protein , 1 types, 1 molecules A

#1: Protein STERYL-SULFATASE / STEROID SULFATASE / STERYL-SULFATE SULFOHYDROLASE / ARYLSULFATASE C / ASC


Mass: 63051.832 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: placenta / References: UniProt: P08842, steryl-sulfatase

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Sugars , 2 types, 4 molecules

#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 132 molecules

#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3.21 Å3/Da / Density % sol: 61.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5
Details: 45-50% MPD, 0.10M ammonium phosphate, pH 8.5, VAPOR DIFFUSION, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
145-50 %MPD1reservoir
2100 mMTris-HCl1reservoirpH8.5
30.10-0.20 Mammonium phosphate1reservoir
40.3 %n-octyl-beta-D-glukopyranoside1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.948
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 14, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.948 Å / Relative weight: 1
ReflectionResolution: 2.6→60 Å / Num. obs: 24534 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 6.1 % / Biso Wilson estimate: 62.5 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.8
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.239 / Mean I/σ(I) obs: 3.1 / Num. unique all: 3482 / % possible all: 96.2
Reflection
*PLUS
Lowest resolution: 60 Å
Reflection shell
*PLUS
% possible obs: 96.2 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 2.6→60 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1183 -RANDOM
Rwork0.254 ---
obs0.254 24533 96.7 %-
all-24533 --
Displacement parametersBiso mean: 58.2 Å2
Refinement stepCycle: LAST / Resolution: 2.6→60 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4337 0 72 130 4539
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.354
X-RAY DIFFRACTIONc_bond_d0.0072
Refinement
*PLUS
Num. reflection obs: 23350 / % reflection Rfree: 4.7 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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