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- PDB-2yhe: Structure determination of the stereoselective inverting sec- alk... -

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Basic information

Entry
Database: PDB / ID: 2yhe
TitleStructure determination of the stereoselective inverting sec- alkylsulfatase Pisa1 from Pseudomonas sp.
ComponentsSEC-ALKYL SULFATASE
KeywordsHYDROLASE / INVERSION / METALLO-BETA-LACTAMASE FOLD
Function / homology
Function and homology information


(R)-specific secondary-alkylsulfatase (type III) / linear primary-alkylsulfatase activity / dodecyl sulfate metabolic process / outer membrane-bounded periplasmic space / protein dimerization activity / metal ion binding
Similarity search - Function
Alkyl sulfatase, dimerisation domain / Metallo-beta-lactamase domain / Alkyl/aryl-sulfatase Bds1/ SdsA1 , MBL-fold / Alkyl sulfatase dimerisation domain / Alkyl sulfatase, C-terminal / Alkyl/aryl-sulfatase, dimerisation domain superfamily / Alkyl sulfatase dimerisation / Alkyl sulfatase C-terminal / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A ...Alkyl sulfatase, dimerisation domain / Metallo-beta-lactamase domain / Alkyl/aryl-sulfatase Bds1/ SdsA1 , MBL-fold / Alkyl sulfatase dimerisation domain / Alkyl sulfatase, C-terminal / Alkyl/aryl-sulfatase, dimerisation domain superfamily / Alkyl sulfatase dimerisation / Alkyl sulfatase C-terminal / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / 4-Layer Sandwich / Alpha Horseshoe / 2-Layer Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(R)-specific secondary-alkylsulfatase
Similarity search - Component
Biological speciesPSEUDOMONAS SP. DSM 6611 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKepplinger, B. / Faber, K. / Macheroux, P. / Schober, M. / Knaus, T. / Wagner, U.G.
CitationJournal: FEBS J. / Year: 2012
Title: Structure and Mechanism of an Inverting Alkylsulfatase from Pseudomonas Sp. Dsm6611 Specific for Secondary Alkylsulfates.
Authors: Knaus, T. / Schober, M. / Kepplinger, B. / Faccinelli, M. / Pitzer, J. / Faber, K. / Macheroux, P. / Wagner, U.
History
DepositionApr 29, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references / Other / Source and taxonomy
Revision 1.2Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.pdbx_dist_value / _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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SEC-ALKYL SULFATASE
B: SEC-ALKYL SULFATASE
C: SEC-ALKYL SULFATASE
D: SEC-ALKYL SULFATASE
E: SEC-ALKYL SULFATASE
F: SEC-ALKYL SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)445,23524
Polymers443,8746
Non-polymers1,36118
Water21,0051166
1
A: SEC-ALKYL SULFATASE
D: SEC-ALKYL SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,4128
Polymers147,9582
Non-polymers4546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10620 Å2
ΔGint-235.2 kcal/mol
Surface area42570 Å2
MethodPISA
2
B: SEC-ALKYL SULFATASE
F: SEC-ALKYL SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,4128
Polymers147,9582
Non-polymers4546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10520 Å2
ΔGint-237.4 kcal/mol
Surface area41980 Å2
MethodPISA
3
C: SEC-ALKYL SULFATASE
E: SEC-ALKYL SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,4128
Polymers147,9582
Non-polymers4546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10600 Å2
ΔGint-232.5 kcal/mol
Surface area41980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.734, 200.587, 245.332
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 4 / Auth seq-ID: 30 - 663 / Label seq-ID: 30 - 663

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

NCS oper:
IDCodeMatrixVector
1given(-0.249837, 0.764882, -0.593748), (-0.461621, -0.633111, -0.621351), (-0.851168, 0.11885, 0.51126)-60.9917, -120.7104, 56.5466
2given(-0.992313, -0.110024, -0.056662), (-0.1215, 0.953153, 0.277015), (0.023529, 0.281769, -0.959194)-76.4738, -3.5725, -8.7597
3given(-0.594236, 0.730788, 0.335906), (0.731135, 0.316785, 0.604226), (0.335151, 0.604645, -0.722549)-40.1734, -7.6862, 65.4187
4given(0.517677, 0.850888, -0.089446), (-0.7411, 0.393714, -0.543838), (-0.427529, 0.34782, 0.83441)-0.303, -70.0944, 43.8148
5given(-0.47255, -0.878411, 0.071346), (-0.845872, 0.42934, -0.316493), (0.247379, -0.209908, -0.945908)-72.9205, -55.982, -68.966

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Components

#1: Protein
SEC-ALKYL SULFATASE


Mass: 73979.016 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS SP. DSM 6611 (bacteria) / Plasmid: PET-21A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): STAR / References: UniProt: F8KAY7
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1166 / 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: 2.11 Å3/Da / Density % sol: 41 % / Description: NONE
Crystal growpH: 4.5
Details: 4 MG/ML PISA1, 18 % W/V PEG 2000, 0.42 MM SODIUM ACETATE PH 4.5 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.1806
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1806 Å / Relative weight: 1
ReflectionResolution: 2.7→19.91 Å / Num. obs: 102022 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 10.1 % / Biso Wilson estimate: 53.427 Å2 / Rmerge(I) obs: 0.17 / Net I/σ(I): 4.4
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SWISS MODEL SERVER

Resolution: 2.7→19.91 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.912 / SU B: 13.063 / SU ML: 0.267 / Cross valid method: THROUGHOUT / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOOP 51-56 IS ILL-DEFINED IN ALL MOLECULES
RfactorNum. reflection% reflectionSelection details
Rfree0.23049 5090 5 %RANDOM
Rwork0.18252 ---
obs0.18492 96842 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.746 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å20 Å20 Å2
2--3.3 Å20 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.7→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29668 0 42 1166 30876
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02230512
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8341.95941436
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.92453859
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.68424.4011445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.686155125
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.39915201
X-RAY DIFFRACTIONr_chiral_restr0.1640.24553
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02123457
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2030.215008
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.220057
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.21686
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0870.220
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1360.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3511.519015
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.424230453
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it8.645311497
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it12.524.510955
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4806 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.310.5
2Bmedium positional0.350.5
3Cmedium positional0.460.5
4Dmedium positional0.350.5
5Emedium positional0.650.5
6Fmedium positional0.350.5
1Amedium thermal7.512
2Bmedium thermal8.352
3Cmedium thermal13.012
4Dmedium thermal6.972
5Emedium thermal6.332
6Fmedium thermal5.382
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 373 -
Rwork0.26 7002 -
obs--99.97 %

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