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- PDB-2x98: H.SALINARUM ALKALINE PHOSPHATASE -

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Basic information

Entry
Database: PDB / ID: 2x98
TitleH.SALINARUM ALKALINE PHOSPHATASE
ComponentsALKALINE PHOSPHATASE
KeywordsHYDROLASE
Function / homology
Function and homology information


alkaline phosphatase / alkaline phosphatase activity / metal ion binding
Similarity search - Function
Diphtheria Toxin Repressor; domain 2 - #40 / Diphtheria Toxin Repressor; domain 2 / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence ...Diphtheria Toxin Repressor; domain 2 - #40 / Diphtheria Toxin Repressor; domain 2 / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Alkaline phosphatase
Similarity search - Component
Biological speciesHALOBACTERIUM SALINARUM (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsWende, A. / Johansson, P. / Grininger, M. / Oesterhelt, D.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural and Biochemical Characterization of a Halophilic Archaeal Alkaline Phosphatase.
Authors: Wende, A. / Johansson, P. / Vollrath, R. / Dyall-Smith, M. / Oesterhelt, D. / Grininger, M.
History
DepositionMar 14, 2010Deposition site: PDBE / Processing site: PDBE
SupersessionMay 19, 2010ID: 2W0Y
Revision 1.0May 19, 2010Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Derived calculations / Refinement description / Version format compliance
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: ALKALINE PHOSPHATASE
B: ALKALINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,50834
Polymers90,2822
Non-polymers1,22632
Water16,988943
1
A: ALKALINE PHOSPHATASE
hetero molecules

A: ALKALINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,44832
Polymers90,2822
Non-polymers1,16630
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7980 Å2
ΔGint-392.5 kcal/mol
Surface area28570 Å2
MethodPISA
2
B: ALKALINE PHOSPHATASE
hetero molecules

B: ALKALINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,56736
Polymers90,2822
Non-polymers1,28634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
Buried area9010 Å2
ΔGint-466 kcal/mol
Surface area28070 Å2
MethodPISA
3
B: ALKALINE PHOSPHATASE
hetero molecules

B: ALKALINE PHOSPHATASE
hetero molecules

A: ALKALINE PHOSPHATASE
hetero molecules

A: ALKALINE PHOSPHATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)183,01568
Polymers180,5644
Non-polymers2,45264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,y,-z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
crystal symmetry operation4_455-x-1/2,y+1/2,-z1
Buried area21160 Å2
ΔGint-853.5 kcal/mol
Surface area52220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.143, 152.524, 86.799
Angle α, β, γ (deg.)90.00, 110.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1482-

NA

21B-1483-

NA

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99996, -0.00238, 0.00824), (0.00236, -0.99999, -0.00225), (0.00824, -0.00223, 0.99996)
Vector: -35.9175, 180.40256, 0.13413)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ALKALINE PHOSPHATASE


Mass: 45140.930 Da / Num. of mol.: 2 / Fragment: RESIDUES 44-474
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HALOBACTERIUM SALINARUM (Halophile) / Strain: R1 / Production host: HALOBACTERIUM SALINARUM (Halophile) / Strain (production host): R1 / References: UniProt: B0R9W3, alkaline phosphatase

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Non-polymers , 6 types, 975 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 24.305 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 943 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDUES 1-43 COMPRISE THE SIGNAL SEQUENCE FOR TAT-MEDIATED EXPORT AND ARE CLEAVED.

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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: 2.36 Å3/Da / Density % sol: 48 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9788
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.7→43.23 Å / Num. obs: 96462 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0053refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→25 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.74 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.19771 6926 7.2 %RANDOM
Rwork0.16042 ---
obs0.16312 89499 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å20 Å20.13 Å2
2---0.15 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6329 0 40 943 7312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216502
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6111.9528890
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345867
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3624.689305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54615918
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9521542
X-RAY DIFFRACTIONr_chiral_restr0.1140.21021
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215136
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_it0.9681.54287
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73926841
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.09532215
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0264.52049
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 515 -
Rwork0.219 6556 -
obs--100 %

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