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- PDB-5a23: SdsA sulfatase triclinic form -

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Basic information

Entry
Database: PDB / ID: 5a23
TitleSdsA sulfatase triclinic form
ComponentsSDS HYDROLASE SDSA1
KeywordsHYDROLASE / SDSA SULFATASE / POLYMORPHS
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 / identical protein binding / 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 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: 2.41 Å
AuthorsDe la Mora, E. / Flores-Hernandez, E. / Jakoncik, 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
DepositionMay 11, 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: SDS HYDROLASE SDSA1
B: SDS HYDROLASE SDSA1
C: SDS HYDROLASE SDSA1
D: SDS HYDROLASE SDSA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,21512
Polymers290,6924
Non-polymers5238
Water00
1
B: SDS HYDROLASE SDSA1
C: SDS HYDROLASE SDSA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,6086
Polymers145,3462
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10690 Å2
ΔGint-184 kcal/mol
Surface area44840 Å2
MethodPISA
2
A: SDS HYDROLASE SDSA1
D: SDS HYDROLASE SDSA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,6086
Polymers145,3462
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-186.5 kcal/mol
Surface area44780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.900, 86.800, 129.030
Angle α, β, γ (deg.)107.59, 102.96, 95.59
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.095, -0.995, 0.01), (-0.995, -0.095, 0.035), (-0.034, -0.013, -0.999)15.52029, 35.0392, -149.76747
2given(-0.101, 0.995, -0.004), (0.994, 0.101, -0.03), (-0.029, -0.006, -1)46.58707, -30.81123, -149.75478
3given(-1, -0.001, -0.003), (0.001, -1, -0.007), (-0.003, -0.007, 1)61.21545, 3.13952, 0.11529

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Components

#1: Protein
SDS HYDROLASE SDSA1 / SDSA ALKYLSULFATASE


Mass: 72673.031 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: Q9I5I9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / 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: 3.32 Å3/Da / Density % sol: 63.1 % / Description: NONE
Crystal growpH: 7
Details: 10% PEG 4000, 10% ISOPROPANOL, 100MM LICL, 100 MM SODIUM CITRATE PH 6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.41→50 Å / Num. obs: 95678 / % possible obs: 71.8 % / Observed criterion σ(I): 1.65 / Redundancy: 2.97 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.34
Reflection shellResolution: 2.41→2.46 Å / Redundancy: 1.94 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.65 / % possible all: 59.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CG3

2cg3


Resolution: 2.41→118.77 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.853 / SU B: 27.741 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R: 0.884 / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30701 4958 5.2 %RANDOM
Rwork0.25349 ---
obs0.25624 90647 71.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.865 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20.12 Å2-0.35 Å2
2--0.6 Å2-0.19 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2.41→118.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19624 0 8 0 19632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01920048
X-RAY DIFFRACTIONr_bond_other_d0.0030.0219048
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9627220
X-RAY DIFFRACTIONr_angle_other_deg1.111343484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.79252496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.00623.2811012
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.164153196
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0615204
X-RAY DIFFRACTIONr_chiral_restr0.0980.22932
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02123304
X-RAY DIFFRACTIONr_gen_planes_other0.0020.024892
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_it2.9544.30810024
X-RAY DIFFRACTIONr_mcbond_other2.9544.30810025
X-RAY DIFFRACTIONr_mcangle_it4.7926.45212512
X-RAY DIFFRACTIONr_mcangle_other4.7926.45212512
X-RAY DIFFRACTIONr_scbond_it2.4934.46210024
X-RAY DIFFRACTIONr_scbond_other2.4934.46210025
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1396.62614709
X-RAY DIFFRACTIONr_long_range_B_refined7.31834.27422874
X-RAY DIFFRACTIONr_long_range_B_other7.31834.27722875
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.41→2.473 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 304 -
Rwork0.334 5513 -
obs--58.87 %
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)
10.1147-0.0030.00020.02420.0140.0217-0.0087-0.0539-0.0243-0.025-0.0028-0.0045-0.0123-0.01640.01140.0280.0010.00830.05890.00630.046214.0327-4.2545-46.1032
20.0983-0.0122-0.03120.06380.00960.02350.01950.01270.0189-0.0114-0.0368-0.0184-0.0166-0.00660.01740.03360.0027-0.00770.02230.01170.05635.41043.8462-105.0003
30.0953-0.051-0.0160.0822-0.04420.0864-0.00630.0157-0.04010.0032-0.03080.01290.01840.00690.03710.03240.0027-0.00150.0197-0.01840.049426.6606-30.3724-104.2693
40.20120.0098-0.03440.0115-0.02470.0710.005-0.0640.0347-0.0053-0.0056-0.01030.0070.02720.00050.0065-0.01090.00310.05030.00040.061747.29147.7629-46.0348
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 524
2X-RAY DIFFRACTION1A530 - 615
3X-RAY DIFFRACTION2B20 - 524
4X-RAY DIFFRACTION2B530 - 615
5X-RAY DIFFRACTION3C20 - 524
6X-RAY DIFFRACTION3C530 - 615
7X-RAY DIFFRACTION4D20 - 524
8X-RAY DIFFRACTION4D530 - 615

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