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- PDB-4a9x: Pseudomonas fluorescens PhoX in complex with the substrate analog... -

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Basic information

Entry
Database: PDB / ID: 4a9x
TitlePseudomonas fluorescens PhoX in complex with the substrate analogue AppCp
ComponentsPHOX
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 / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / MU-OXO-DIIRON / Transcriptional initiation protein Tat
Function and homology information
Biological speciesPSEUDOMONAS FLUORESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 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
DepositionNov 29, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Sep 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

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Assembly

Deposited unit
A: PHOX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5118
Polymers64,6341
Non-polymers8777
Water9,440524
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.400, 78.900, 111.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PHOX / ALKALINE PHOSPHATASE


Mass: 64633.547 Da / Num. of mol.: 1 / 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 , 5 types, 531 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-FEO / MU-OXO-DIIRON


Mass: 127.689 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 524 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsPF15179 IN ORLN DATABASE

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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: 2.44 Å3/Da / Density % sol: 49.5 % / Description: NONE
Crystal growpH: 7.9
Details: 19% PEG 6000, 0.1 M TRIS PH 7.9, 0.2 M LICL, 300 UM CACL2, 1.5 MM APPCP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97932
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 11, 2011 / Details: CYLINDRICAL GRAZING INCIDENCE MIRROR
RadiationMonochromator: SI(311) AND SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.79→64.43 Å / Num. obs: 53322 / % possible obs: 90.1 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 15.97 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6.8
Reflection shellResolution: 1.79→1.84 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.9 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4A9V

4a9v


Resolution: 1.79→35.8 Å / Cor.coef. Fo:Fc: 0.8619 / Cor.coef. Fo:Fc free: 0.7979 / SU R Cruickshank DPI: 0.275 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.189 / SU Rfree Blow DPI: 0.17 / SU Rfree Cruickshank DPI: 0.168
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=FE CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9438. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=FE CA. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=9438. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=0. NUMBER TREATED BY BAD NON-BONDED CONTACTS=5.
RfactorNum. reflection% reflectionSelection details
Rfree0.2866 2614 5.06 %RANDOM
Rwork0.2428 ---
obs0.2451 51706 87.25 %-
Displacement parametersBiso mean: 18.48 Å2
Baniso -1Baniso -2Baniso -3
1--1.8853 Å20 Å20 Å2
2--1.2594 Å20 Å2
3---0.6259 Å2
Refine analyzeLuzzati coordinate error obs: 0.439 Å
Refinement stepCycle: LAST / Resolution: 1.79→35.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4469 0 45 524 5038
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.019025HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1116231HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1914SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes133HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1434HARMONIC5
X-RAY DIFFRACTIONt_it9025HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.8
X-RAY DIFFRACTIONt_other_torsion14.25
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion582SEMIHARMONIC5
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_contact10099SEMIHARMONIC4
LS refinement shellResolution: 1.79→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2509 205 4.97 %
Rwork0.2189 3919 -
all0.2206 4124 -
obs--87.25 %

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