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- PDB-3a52: Crystal structure of cold-active alkailne phosphatase from psychr... -

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Basic information

Entry
Database: PDB / ID: 3a52
TitleCrystal structure of cold-active alkailne phosphatase from psychrophile Shewanella sp.
ComponentsCold-active alkaline phosphatase
KeywordsHYDROLASE / phosphatase
Function / homology
Function and homology information


phosphatase activity / metal ion binding
Similarity search - Function
Diphtheria Toxin Repressor; domain 2 - #40 / Diphtheria Toxin Repressor; domain 2 / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily ...Diphtheria Toxin Repressor; domain 2 - #40 / Diphtheria Toxin Repressor; domain 2 / Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Cold-active alkaline phosphatase
Similarity search - Component
Biological speciesShewanella (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsTsuruta, H. / Mikami, B. / Higashi, T. / Aizono, Y.
CitationJournal: Biosci.Biotechnol.Biochem. / Year: 2010
Title: Crystal structure of cold-active alkaline phosphatase from the psychrophile Shewanella sp.
Authors: Tsuruta, H. / Mikami, B. / Higashi, T. / Aizono, Y.
History
DepositionJul 24, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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_asym_id / _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_asym_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_ref_seq_dif.details / _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: Cold-active alkaline phosphatase
B: Cold-active alkaline phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,80911
Polymers86,2932
Non-polymers5169
Water14,430801
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-191 kcal/mol
Surface area28220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.059, 95.863, 71.058
Angle α, β, γ (deg.)90.000, 101.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Cold-active alkaline phosphatase


Mass: 43146.359 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella (bacteria) / Strain: AP1 / Gene: scap / Production host: Escherichia coli (E. coli) / References: UniProt: Q8RQU7
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#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.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 801 / 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: 2.48 Å3/Da / Density % sol: 50.33 % / Mosaicity: 1.175 °
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: PEG 8000, ammonium sulfate, glycerol, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jan 1, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 41352 / % possible obs: 97.5 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.089 / Χ2: 0.702 / Net I/σ(I): 15.378
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.221 / Num. unique all: 3914 / Χ2: 0.467 / % possible all: 92.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→15 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.244 4152 9.7 %
Rwork0.183 --
obs-41211 96.7 %
Solvent computationBsol: 61.673 Å2
Displacement parametersBiso max: 43.26 Å2 / Biso mean: 12.968 Å2 / Biso min: 1 Å2
Baniso -1Baniso -2Baniso -3
1--3.563 Å20 Å2-1.048 Å2
2--0.603 Å20 Å2
3---2.96 Å2
Refinement stepCycle: LAST / Resolution: 2.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6040 0 21 801 6862
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1871.5
X-RAY DIFFRACTIONc_scbond_it2.0252
X-RAY DIFFRACTIONc_mcangle_it1.7642
X-RAY DIFFRACTIONc_scangle_it2.8382.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3carbohydrate.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5so4.param

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