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- PDB-6qsq: X-ray crystal structure of the R336L Vibrio alkaline phosphatase ... -

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Basic information

Entry
Database: PDB / ID: 6qsq
TitleX-ray crystal structure of the R336L Vibrio alkaline phosphatase variant.
ComponentsAlkaline phosphatase
KeywordsHYDROLASE / Enzyme dynamics Disordered loop Homodimer
Function / homology
Function and homology information


phosphatase activity
Similarity search - Function
Alkaline phosphatase, crown domain / Alkaline phosphatase, crown domain / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A ...Alkaline phosphatase, crown domain / Alkaline phosphatase, crown domain / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A / Alkaline-phosphatase-like, core domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-DTB / Alkaline phosphatase
Similarity search - Component
Biological speciesVibrio splendidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsHjorleifsson, J.G. / Helland, R. / Asgeirsson, B.
Funding support Iceland, Norway, 2items
OrganizationGrant numberCountry
Other government141619-051 Iceland
Research Council of Norway247732 Norway
CitationJournal: Febs Open Bio / Year: 2020
Title: The high catalytic rate of the cold-active Vibrio alkaline phosphatase requires a hydrogen bonding network involving a large interface loop.
Authors: Hjorleifsson, J.G. / Helland, R. / Magnusdottir, M. / Asgeirsson, B.
History
DepositionFeb 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0606
Polymers56,5941
Non-polymers4655
Water4,252236
1
A: Alkaline phosphatase
hetero molecules

A: Alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,11912
Polymers113,1882
Non-polymers93110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area10130 Å2
ΔGint-233 kcal/mol
Surface area32660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.082, 118.596, 83.922
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Alkaline phosphatase /


Mass: 56594.102 Da / Num. of mol.: 1 / Mutation: R336L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio splendidus (bacteria) / Gene: BCT36_11160 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2N7KUA1

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Non-polymers , 5 types, 241 molecules

#2: Chemical ChemComp-DTB / 6-(5-METHYL-2-OXO-IMIDAZOLIDIN-4-YL)-HEXANOIC ACID / D-DESTHIOBIOTIN


Mass: 214.262 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H18N2O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.2 Å3/Da / Density % sol: 44.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Reservoir conditions 20%(w/v) PEG 3350 and 0.2 M potassium formate. Protein conditions: 20 mM Tris, 1 mM MgSO4, 5 mM MgCl2, 1.3 mM desthiobiotin, 0.25 M NaCl, 15 % (v/v) ethylene glycol, pH 8.0.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 2→48.43 Å / Num. obs: 33403 / % possible obs: 100 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Rrim(I) all: 0.069 / Net I/σ(I): 20.7 / Num. measured all: 222083
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2-2.056.90.52624230.8610.2160.56999.9
8.94-48.435.30.0234220.9990.0110.02698.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALA0.5.8data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E2D

3e2d


Resolution: 2→48.43 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.398 / SU ML: 0.12 / SU R Cruickshank DPI: 0.1767 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.159
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2182 1610 4.8 %RANDOM
Rwork0.1688 ---
obs0.1712 31771 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 78.51 Å2 / Biso mean: 30.28 Å2 / Biso min: 9.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-0 Å2
2---0.38 Å2-0 Å2
3---0.9 Å2
Refinement stepCycle: final / Resolution: 2→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3809 0 23 236 4068
Biso mean--41.8 34.5 -
Num. residues----503
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0193927
X-RAY DIFFRACTIONr_bond_other_d0.0010.023583
X-RAY DIFFRACTIONr_angle_refined_deg1.8371.9515338
X-RAY DIFFRACTIONr_angle_other_deg0.88738239
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.685506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83225.604182
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.93415617
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0061512
X-RAY DIFFRACTIONr_chiral_restr0.1090.2591
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024609
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02897
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 117 -
Rwork0.242 2304 -
all-2421 -
obs--99.88 %

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