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- PDB-3zwu: Pseudomonas fluorescens PhoX in complex with vanadate, a transiti... -

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Basic information

Entry
Database: PDB / ID: 3zwu
TitlePseudomonas fluorescens PhoX in complex with vanadate, a transition state analogue
ComponentsALKALINE PHOSPHATASE PHOX
KeywordsHYDROLASE / BETA-PROPELLER / IRON
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 / VANADATE ION / Transcriptional initiation protein Tat
Function and homology information
Biological speciesPSEUDOMONAS FLUORESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.39 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
DepositionAug 2, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Sep 17, 2014Group: Database references
Revision 1.3May 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_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)130,13516
Polymers129,2672
Non-polymers86814
Water30,7341706
1
A: ALKALINE PHOSPHATASE PHOX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0678
Polymers64,6341
Non-polymers4347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ALKALINE PHOSPHATASE PHOX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0678
Polymers64,6341
Non-polymers4347
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.790, 71.470, 227.830
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: (0.097225, -0.994808, 0.030085), (-0.994864, -0.097997, -0.025352), (0.028168, -0.027465, -0.999226)
Vector: 16.7969, 20.1071, 56.7149)

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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 , 5 types, 1720 molecules

#2: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: VO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


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


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


Mass: 127.689 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe2O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1706 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsVANADATE (VO4): TRANSITION STATE ANALOGUE CALCIUM ION (CA): CATALYTIC SITE FE (III) ION (FE): CATALYTIC SITE
Sequence detailsSEQUENCE CORRESPONDS TO ENTRY PF15179 IN ORLN DATABASE. FRAGMENT SEQUENCE CORRESPONDS TO MATURE ...SEQUENCE CORRESPONDS TO ENTRY PF15179 IN ORLN DATABASE. FRAGMENT SEQUENCE CORRESPONDS TO MATURE EXPORTED PROTEIN.

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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: 2.2 Å3/Da / Density % sol: 44.13 %
Description: PHASED WITH LUTHENIUM CO-CRYSTALS COLLECTED AT THE LU EDGE
Crystal growpH: 8
Details: 0.1 M TRIS HCL PH 8.0, 0.2 M LICL, 20% W/V PEG 6000, 100 UM NA3 VO4.

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9395
DetectorType: ADSC / Date: Feb 22, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9395 Å / Relative weight: 1
ReflectionResolution: 1.39→38.42 Å / Num. obs: 223863 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 14.2 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.4
Reflection shellResolution: 1.39→1.43 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.7 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.1refinement
XDSdata reduction
SCALAdata scaling
SHELXDphasing
SHARPphasing
SOLOMONphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.39→38.42 Å / Cor.coef. Fo:Fc: 0.9658 / Cor.coef. Fo:Fc free: 0.9587 / SU R Cruickshank DPI: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.055 / SU Rfree Blow DPI: 0.053 / SU Rfree Cruickshank DPI: 0.052
Details: OCCUPANCY REFINEMENT ON IONS. REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=FE CA VO4 CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM ...Details: OCCUPANCY REFINEMENT ON IONS. REFINEMENT NOTE 1: IDEAL-DIST CONTACT TERM CONTACT SETUP. RESIDUE TYPES WITHOUT CCP4 ATOM TYPE IN LIBRARY=FE CA VO4 CL. NUMBER OF ATOMS WITH PROPER CCP4 ATOM TYPE=19237. NUMBER WITH APPROX DEFAULT CCP4 ATOM TYPE=8. NUMBER TREATED BY BAD NON-BONDED CONTACTS=16.
RfactorNum. reflection% reflectionSelection details
Rfree0.1713 11275 5.04 %RANDOM
Rwork0.158 ---
obs0.1586 223750 99.08 %-
Displacement parametersBiso mean: 15.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.5412 Å20 Å20 Å2
2---0.5691 Å20 Å2
3---0.028 Å2
Refine analyzeLuzzati coordinate error obs: 0.142 Å
Refinement stepCycle: LAST / Resolution: 1.39→38.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8926 0 26 1706 10658
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00617771HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9931890HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3739SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes261HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2783HARMONIC5
X-RAY DIFFRACTIONt_it17771HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.66
X-RAY DIFFRACTIONt_other_torsion13.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1143SEMIHARMONIC5
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_contact21347SEMIHARMONIC4
LS refinement shellResolution: 1.39→1.43 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2324 822 5.31 %
Rwork0.2242 14665 -
all0.2247 15487 -
obs--99.08 %

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