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- PDB-5ajl: Sdsa sulfatase tetragonal -

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Basic information

Entry
Database: PDB / ID: 5ajl
TitleSdsa sulfatase tetragonal
ComponentsALKYL SULFATASE
KeywordsHYDROLASE / POLYMORPHS / CRYSTAL CONTACTS
Function / homology
Function and homology information


linear primary-alkylsulfatase / linear primary-alkylsulfatase activity / dodecyl sulfate metabolic process / outer membrane-bounded periplasmic space / protein dimerization activity / metal ion binding / identical protein binding
Similarity search - Function
Alkyl sulfatase, dimerisation domain / Metallo-beta-lactamase domain / : / Alkyl sulfatase dimerisation domain / Alkyl sulfatase, C-terminal / Alkyl/aryl-sulfatase, dimerisation domain superfamily / Alkyl/aryl-sulfatase Bds1/ SdsA1 , MBL-fold / Alkyl sulfatase dimerisation / Alkyl sulfatase C-terminal / SCP2 sterol-binding domain ...Alkyl sulfatase, dimerisation domain / Metallo-beta-lactamase domain / : / Alkyl sulfatase dimerisation domain / Alkyl sulfatase, C-terminal / Alkyl/aryl-sulfatase, dimerisation domain superfamily / Alkyl/aryl-sulfatase Bds1/ SdsA1 , MBL-fold / 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 superfamily / Metallo-beta-lactamase; Chain A / 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
Linear primary-alkylsulfatase / :
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsDe la Mora, E. / Flores-Hernandez, E. / Jakoncic, J. / Stojanoff, V. / Sanchez-Puig, N. / Moreno, A.
CitationJournal: J.Appl.Crystallogr. / Year: 2015
Title: Sdsa Polymorph Isolation and Improvement of Their Crystal Quality Using Nonconventional Crystallization Techniques
Authors: De La Mora, E. / Flores-Hernandez, E. / Jakoncic, J. / Stojanoff, V. / Siliqi, D. / Sanchez-Puig, N. / Moreno, A.
History
DepositionFeb 25, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 10, 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_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_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_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_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: ALKYL SULFATASE
B: ALKYL SULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,6086
Polymers145,3462
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10610 Å2
ΔGint-194.3 kcal/mol
Surface area46300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.580, 88.580, 193.930
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein ALKYL SULFATASE / SDSA ALKYLSULFATASE


Mass: 72673.031 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: V9UAA9, UniProt: Q9I5I9*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 2.7 Å3/Da / Density % sol: 53.8 % / Description: NONE
Crystal growpH: 7
Details: 12% PEG 4000, 10% ISOPROPANOL, 200 MM LICL, 100 MM CITRATE BUFFER PH 6.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.078
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 3.48→20 Å / Num. obs: 18672 / % possible obs: 97.6 % / Observed criterion σ(I): 1.65 / Redundancy: 5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.11
Reflection shellResolution: 3.48→3.68 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.65 / % possible all: 88.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CG3

2cg3


Resolution: 3.45→52.61 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.88 / SU B: 123.296 / SU ML: 0.784 / Cross valid method: THROUGHOUT / ESU R Free: 0.739 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28901 1005 5.1 %RANDOM
Rwork0.24411 ---
obs0.24638 18616 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 130.155 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2---0.99 Å20 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 3.45→52.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9842 0 4 0 9846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01910074
X-RAY DIFFRACTIONr_bond_other_d0.0020.029572
X-RAY DIFFRACTIONr_angle_refined_deg1.2521.9613684
X-RAY DIFFRACTIONr_angle_other_deg0.973321854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.79751260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40923.281506
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.204151604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.60415102
X-RAY DIFFRACTIONr_chiral_restr0.0710.21474
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02111736
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022458
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7136.5985048
X-RAY DIFFRACTIONr_mcbond_other0.7136.5985049
X-RAY DIFFRACTIONr_mcangle_it1.2789.8956308
X-RAY DIFFRACTIONr_mcangle_other1.2789.8956308
X-RAY DIFFRACTIONr_scbond_it0.5726.6565026
X-RAY DIFFRACTIONr_scbond_other0.5726.6575027
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.0629.967377
X-RAY DIFFRACTIONr_long_range_B_refined2.57151.98411243
X-RAY DIFFRACTIONr_long_range_B_other2.57151.98611244
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.45→3.54 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 86 -
Rwork0.343 1370 -
obs--99.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.8636-0.360.15442.28360.01393.37190.20030.2116-0.2232-1.1071-0.32850.9595-0.18170.2120.12820.57960.0585-0.49530.3185-0.07440.4258-6.724329.5697-8.5697
21.7946-0.35550.09162.32430.42742.7689-0.0559-0.51020.43340.1513-0.1532-0.0106-1.17160.73090.20910.5992-0.3843-0.18220.5916-0.02890.29075.25147.57218.2821
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 655
2X-RAY DIFFRACTION2B20 - 655

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