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- PDB-4amf: Pseudomonas fluorescens PhoX in complex with the substrate analog... -

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Basic information

Entry
Database: PDB / ID: 4amf
TitlePseudomonas fluorescens PhoX in complex with the substrate analogue AppCp
ComponentsPHOX
KeywordsHYDROLASE / ALKALINE PHOSPHATASE / PHOX / BETA- PROPELLER / IRON / APPCP / SUBSTRATE ANALOGUE / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
Function / homology
Function and homology information


Alkaline phosphatase PhoX / Alkaline phosphatase PhoX / Six-bladed beta-propeller, TolB-like / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / MU-OXO-DIIRON / : / Transcriptional initiation protein Tat
Similarity search - Component
Biological speciesPSEUDOMONAS FLUORESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 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 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 30, 2014Group: Database references
Revision 1.2Sep 10, 2014Group: Database references
Revision 1.3Sep 17, 2014Group: Database references
Revision 2.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _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: PHOX
B: PHOX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,22132
Polymers128,6082
Non-polymers2,61330
Water21,9421218
1
A: PHOX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,69418
Polymers64,3041
Non-polymers1,39017
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PHOX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,52714
Polymers64,3041
Non-polymers1,22313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.490, 70.380, 227.870
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: (0.084252, -0.996433, 0.004791), (-0.996242, -0.084331, -0.019748), (0.020082, -0.003109, -0.999794)
Vector: 17.0982, 18.9888, 56.8495)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PHOX


Mass: 64304.242 Da / Num. of mol.: 2 / Fragment: YES
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH APPCP / Source: (gene. exp.) PSEUDOMONAS FLUORESCENS (bacteria) / Strain: PF0-1 / Plasmid: PQE60-PHOX AND PREP4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C43 DELTA TAT / References: UniProt: Q3K5N8, alkaline phosphatase

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Non-polymers , 7 types, 1248 molecules

#2: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-LI / LITHIUM ION


Mass: 6.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Li
#5: Chemical
ChemComp-CA / CALCIUM ION


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


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


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1218 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsHIS-TAGGED AT THE C-TERMINUS

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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: 19% PEG 6000, 0.1 M TRIS PH 7.9, 0.2 M LICL, 300 UM CACL2, SOAKED IN APPCP 1MM

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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: 1.52→70.38 Å / Num. obs: 166380 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.9
Reflection shellResolution: 1.52→1.56 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 3.2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
BUSTER-TNTBUSTER 2.11.2refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A9X

4a9x


Resolution: 1.52→67.25 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU R Cruickshank DPI: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.07 / SU Rfree Blow DPI: 0.071 / SU Rfree Cruickshank DPI: 0.07 / Details: REMARK 3 NULL
RfactorNum. reflection% reflectionSelection details
Rfree0.1831 8352 5 %RANDOM
Rwork0.1547 ---
obs0.1561 166094 97.77 %-
Displacement parametersBiso mean: 18.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.4733 Å20 Å20 Å2
2--0.596 Å20 Å2
3---0.8773 Å2
Refine analyzeLuzzati coordinate error obs: 0.143 Å
Refinement stepCycle: LAST / Resolution: 1.52→67.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8938 0 142 1218 10298
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0118473HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1133275HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3967SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes268HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2945HARMONIC5
X-RAY DIFFRACTIONt_it18473HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.53
X-RAY DIFFRACTIONt_other_torsion14.08
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1187SEMIHARMONIC5
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_contact21966SEMIHARMONIC4
LS refinement shellResolution: 1.52→1.56 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2375 560 5.24 %
Rwork0.1966 10132 -
all0.1987 10692 -
obs--97.77 %

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