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- PDB-4alf: Pseudomonas fluorescens PhoX in complex with phosphate -

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Basic information

Entry
Database: PDB / ID: 4alf
TitlePseudomonas fluorescens PhoX in complex with phosphate
ComponentsALKALINE PHOSPHATASE PHOX
KeywordsHYDROLASE / BETA-PROPELLER
Function / homologyAlkaline phosphatase PhoX / Alkaline phosphatase PhoX / Six-bladed beta-propeller, TolB-like / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / metal ion binding / MU-OXO-DIIRON / PHOSPHATE ION / Transcriptional initiation protein Tat
Function and homology information
Biological speciesPSEUDOMONAS FLUORESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsYong, S.C. / Roversi, P. / Lillington, J.E.D. / Zeldin, O.B. / Garman, E.F. / Lea, S.M. / Berks, B.C.
CitationJournal: Science / Year: 2014
Title: A Complex Iron-Calcium Cofactor Catalyzing Phosphotransfer Chemistry
Authors: Yong, S.C. / Roversi, P. / Lillington, J. / Rodriguez, F. / Krehenbrink, M. / Zeldin, O.B. / Garman, E.F. / Lea, S.M. / Berks, B.C.
History
DepositionMar 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3Dec 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_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_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_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

Downloads & links

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Assembly

Deposited unit
A: ALKALINE PHOSPHATASE PHOX
B: ALKALINE PHOSPHATASE PHOX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,07931
Polymers129,2672
Non-polymers1,81229
Water25,3651408
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A: ALKALINE PHOSPHATASE PHOX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,63317
Polymers64,6341
Non-polymers99916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALKALINE PHOSPHATASE PHOX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,44614
Polymers64,6341
Non-polymers81313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.099, 71.035, 228.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.083774, -0.996375, 0.014773), (-0.99643, -0.083915, -0.009232), (0.010438, -0.013947, -0.999848)
Vector: 16.8473, 19.1794, 57.068)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein ALKALINE PHOSPHATASE PHOX


Mass: 64633.547 Da / Num. of mol.: 2 / Fragment: RESIDUES 48-633
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: PF0-1 / Plasmid: PQE60-PHOX AND PREP4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / Variant (production host): C43 DELTA TAT / References: UniProt: Q3K5N8, alkaline phosphatase

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Non-polymers , 6 types, 1437 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2O
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1408 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsCOMPLEX WITH ORTHOPHOSPHATE
Sequence detailsCTERMINALLY HIS-TAGGED, NO SIGNAL PEPTIDE

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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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 8
Details: 0.1 M TRIS HCL PH 8.0, 0.2 M LICL, REMARK 280 20% W/V PEG 6000. THE CRYSTALS WERE SOAKED WITH 100 UL PHOSPHATE BUFFERED SALINE FOR HALF AN HOUR

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.25→16.2 Å / Num. obs: 258332 / % possible obs: 83.6 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 6.3
Reflection shellResolution: 1.25→1.31 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / % possible all: 74.3

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ZWU

3zwu


Resolution: 1.25→16.14 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.4 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES REFINED INDIVIDUALLY. OCCUPANCY REFINEMENT IN AUTOBUSTER PRIOR TO REFMAC5 REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.16432 12913 5 %RANDOM
Rwork0.13272 ---
obs0.1343 243880 82.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.36 Å20 Å20 Å2
2---0.34 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.25→16.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8938 0 92 1408 10438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0199644
X-RAY DIFFRACTIONr_bond_other_d0.0010.029099
X-RAY DIFFRACTIONr_angle_refined_deg1.4631.93813106
X-RAY DIFFRACTIONr_angle_other_deg0.8083.00120709
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.38451277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.03524.082490
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.491151549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0571575
X-RAY DIFFRACTIONr_chiral_restr0.0880.21322
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02111494
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022352
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_restr2.37118743
X-RAY DIFFRACTIONr_sphericity_free22.5415335
X-RAY DIFFRACTIONr_sphericity_bonded6.49819553
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 848 -
Rwork0.213 15060 -
obs--72.56 %

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