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- PDB-4axh: Structure and mechanism of the first inverting alkylsulfatase spe... -

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Basic information

Entry
Database: PDB / ID: 4axh
TitleStructure and mechanism of the first inverting alkylsulfatase specific for secondary alkylsulfatases
ComponentsSEC-ALKYLSULFATASE
KeywordsHYDROLASE / REACTION MECHANISM / ZINC-DEPENDENT
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 / MAD / Resolution: 2.7 Å
AuthorsKnaus, T. / Schober, M. / Faber, K. / Macheroux, P. / 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
DepositionJun 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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_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

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Assembly

Deposited unit
A: SEC-ALKYLSULFATASE
B: SEC-ALKYLSULFATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,3167
Polymers147,9582
Non-polymers3585
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10360 Å2
ΔGint-217.9 kcal/mol
Surface area42910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)141.980, 141.980, 119.680
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.42219, 0.471121, -0.774468), (0.442004, -0.638918, -0.629616), (-0.791447, -0.608135, 0.061508)
Vector: -63.607, 49.755, -17.38)

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Components

#1: Protein SEC-ALKYLSULFATASE


Mass: 73979.016 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-660
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS SP. DSM 6611 (bacteria) / 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.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.34 Å3/Da / Density % sol: 47 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.18076
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 21, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.18076 Å / Relative weight: 1
ReflectionResolution: 2.7→19.93 Å / Num. obs: 36072 / % possible obs: 93.3 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Biso Wilson estimate: 65.35 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.8
Reflection shellResolution: 2.7→8.54 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 3.1 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.7→19.59 Å / Cor.coef. Fo:Fc: 0.9211 / Cor.coef. Fo:Fc free: 0.8849 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.377
Details: B32-B193, B261-B308, B336-B37 DEFINED AND WERE MODELLED AS NCS-MATES FROM MOLECULE A. IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ...Details: B32-B193, B261-B308, B336-B37 DEFINED AND WERE MODELLED AS NCS-MATES FROM MOLECULE A. IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=ZN. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=10041. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=4. FOR ATOMS IN HIGHLY DISORDERED REGIONS AN OCCUPANCY OF 0.5 WAS CHOOSEN.
RfactorNum. reflection% reflectionSelection details
Rfree0.2659 1803 5.01 %RANDOM
Rwork0.2209 ---
obs0.2231 36015 93.54 %-
Displacement parametersBiso mean: 77.7 Å2
Baniso -1Baniso -2Baniso -3
1--5.3915 Å20 Å20 Å2
2---5.3915 Å20 Å2
3---10.783 Å2
Refine analyzeLuzzati coordinate error obs: 0.443 Å
Refinement stepCycle: LAST / Resolution: 2.7→19.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9813 0 9 136 9958
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0110128HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2313759HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3540SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes278HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1487HARMONIC5
X-RAY DIFFRACTIONt_it10128HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.79
X-RAY DIFFRACTIONt_other_torsion22.07
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1294SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11930SEMIHARMONIC4
LS refinement shellResolution: 2.7→2.78 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.3219 154 4.93 %
Rwork0.2812 2968 -
all0.2832 3122 -
obs--93.54 %

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