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- PDB-4av7: Structure determination of the double mutant S233Y F250G from the... -

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Basic information

Entry
Database: PDB / ID: 4av7
TitleStructure determination of the double mutant S233Y F250G from the sec- alkyl sulfatase PisA1
ComponentsSEC-ALKYLSULFATASE
KeywordsHYDROLASE / INVERTING ALKYLSULFATASE / DOUBLE MUTANT
Function / homology
Function and homology information


(R)-specific secondary-alkylsulfatase (type III) / linear primary-alkylsulfatase activity / dodecyl sulfate metabolic process / protein dimerization activity / metal ion 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
(R)-specific secondary-alkylsulfatase
Similarity search - Component
Biological speciesPSEUDOMONAS SP. DSM 6611 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKnaus, T. / Schober, M. / Faber, K. / Macharaux, P. / Wagner, U.
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
DepositionMay 24, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: 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: SEC-ALKYLSULFATASE
B: SEC-ALKYLSULFATASE
C: SEC-ALKYLSULFATASE
D: SEC-ALKYLSULFATASE
E: SEC-ALKYLSULFATASE
F: SEC-ALKYLSULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)445,15124
Polymers443,7906
Non-polymers1,36118
Water5,729318
1
A: SEC-ALKYLSULFATASE
D: SEC-ALKYLSULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3848
Polymers147,9302
Non-polymers4546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10610 Å2
ΔGint-236.1 kcal/mol
Surface area43010 Å2
MethodPISA
2
B: SEC-ALKYLSULFATASE
C: SEC-ALKYLSULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3848
Polymers147,9302
Non-polymers4546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10610 Å2
ΔGint-235.3 kcal/mol
Surface area43570 Å2
MethodPISA
3
E: SEC-ALKYLSULFATASE
F: SEC-ALKYLSULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3848
Polymers147,9302
Non-polymers4546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10610 Å2
ΔGint-235.8 kcal/mol
Surface area42950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.201, 201.955, 248.495
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.991912, -0.109204, -0.064694), (-0.083931, 0.946663, -0.311104), (0.095217, -0.303158, -0.948172)69.5811, 0.7086, -12.7146
2given(0.532939, 0.830037, 0.164361), (-0.765649, 0.390357, 0.511275), (0.360218, -0.398322, 0.843554)2.4457, 68.9155, 48.1986
3given(-0.624403, 0.689533, -0.366966), (0.693901, 0.273959, -0.665919), (-0.35864, -0.67044, -0.649529)41.3014, 12.1663, 65.6883
4given(-0.224766, 0.760917, 0.608675), (-0.462722, -0.633083, 0.62056), (0.857536, -0.142167, 0.494388)61.9279, 122.413, 54.6124
5given(-0.481858, -0.864228, -0.144644), (-0.861727, 0.437443, 0.25704), (-0.158868, 0.248501, -0.955515)65.9139, 52.3863, -74.4509

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Components

#1: Protein
SEC-ALKYLSULFATASE / PISA1-DM / SECONDARY ALKYLSULFATASE


Mass: 73964.984 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS SP. DSM 6611 (bacteria) / Description: GERMAN COLLECTION OF MICROORGANISMS DSM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / 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.: 318 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 233 TO TYR ENGINEERED RESIDUE IN CHAIN A, PHE 250 TO GLY ...ENGINEERED RESIDUE IN CHAIN A, SER 233 TO TYR ENGINEERED RESIDUE IN CHAIN A, PHE 250 TO GLY ENGINEERED RESIDUE IN CHAIN B, SER 233 TO TYR ENGINEERED RESIDUE IN CHAIN B, PHE 250 TO GLY ENGINEERED RESIDUE IN CHAIN C, SER 233 TO TYR ENGINEERED RESIDUE IN CHAIN C, PHE 250 TO GLY ENGINEERED RESIDUE IN CHAIN D, SER 233 TO TYR ENGINEERED RESIDUE IN CHAIN D, PHE 250 TO GLY ENGINEERED RESIDUE IN CHAIN E, SER 233 TO TYR ENGINEERED RESIDUE IN CHAIN E, PHE 250 TO GLY

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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: 2.16 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growpH: 4.5
Details: 10 MG/ML PROTEIN, 0.1 M SODIUM ACETATE PH 4.7, 30% W/V PEG 2000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 1.00441
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00441 Å / Relative weight: 1
ReflectionResolution: 2.95→48.76 Å / Num. obs: 79645 / % possible obs: 78.4 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.8
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 2 / % possible all: 79.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YHE

2yhe


Resolution: 3→45.65 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.908 / SU B: 47.029 / SU ML: 0.43 / Cross valid method: THROUGHOUT / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT ALL CHAINS HAVE DISORDERED REGIONS WITH HIGH B-FACTOR DISORDERED REGIONS WERE MODELED VIA NCS
RfactorNum. reflection% reflectionSelection details
Rfree0.25591 3839 5 %RANDOM
Rwork0.18646 ---
obs0.19 72749 99.75 %-
Displacement parametersBiso mean: 86.832 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--1.03 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 3→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29640 0 42 318 30000
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0230304
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.9641110
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.05853801
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79224.3791425
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.289155068
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.13515198
X-RAY DIFFRACTIONr_chiral_restr0.0870.24516
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02123255
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 261 -
Rwork0.325 4918 -
obs--99.85 %

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