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- PDB-5i84: Structure of the Xanthomonas citri phosphate-binding protein PhoX -

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Basic information

Entry
Database: PDB / ID: 5i84
TitleStructure of the Xanthomonas citri phosphate-binding protein PhoX
ComponentsPhosphate-binding protein PstS
KeywordsTRANSPORT PROTEIN / ABC transporter / periplasmic-binding protein / phosphate-binding protein / PhoX
Function / homology
Function and homology information


phosphate ion transmembrane transport / phosphate ion binding / ATP-binding cassette (ABC) transporter complex
Similarity search - Function
Phosphate ABC transporter, substrate-binding protein PstS / PBP superfamily domain / PBP domain / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Phosphate-binding protein PstS
Similarity search - Component
Biological speciesXanthomonas axonopodis pv. citri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.98 Å
AuthorsPegos, V.R. / Medrano, F.J. / Balan, A.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2011-20468-1 Brazil
Citation
Journal: To Be Published
Title: A gene duplication in phosphate-binding proteins from pho regulon of Xanthomonas citri: functional and structural studies
Authors: Pegos, V.R. / Santos, R.M.L. / Medrano, F.J. / Balan, A.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Crystallization and preliminary X-ray diffraction analysis of the phosphate-binding protein PhoX from Xanthomonas citri.
Authors: Pegos, V.R. / Medrano, F.J. / Balan, A.
History
DepositionFeb 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Data collection
Revision 1.2Aug 9, 2017Group: Database references / Derived calculations / Category: pdbx_related_exp_data_set / pdbx_struct_oper_list / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphate-binding protein PstS
B: Phosphate-binding protein PstS
C: Phosphate-binding protein PstS
D: Phosphate-binding protein PstS
E: Phosphate-binding protein PstS
F: Phosphate-binding protein PstS
G: Phosphate-binding protein PstS
H: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,14842
Polymers282,9198
Non-polymers3,22934
Water50428
1
A: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7455
Polymers35,3651
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8406
Polymers35,3651
Non-polymers4755
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7455
Polymers35,3651
Non-polymers3804
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8406
Polymers35,3651
Non-polymers4755
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8406
Polymers35,3651
Non-polymers4755
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9357
Polymers35,3651
Non-polymers5706
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5553
Polymers35,3651
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Phosphate-binding protein PstS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6504
Polymers35,3651
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.556, 115.643, 133.323
Angle α, β, γ (deg.)90.00, 90.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Phosphate-binding protein PstS


Mass: 35364.879 Da / Num. of mol.: 8 / Fragment: residues 25-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas axonopodis pv. citri (bacteria)
Strain: 306 / Gene: phoX, XAC1578 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8PM55
#2: Chemical...
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 34 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / Details: 200 mM sodium iodide 20% PEG 3350

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.459 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.459 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.615
11-h,-k,l20.385
ReflectionResolution: 2.98→87.36 Å / Num. obs: 46810 / % possible obs: 94.3 % / Redundancy: 2.8 % / Net I/σ(I): 8.4
Reflection shellResolution: 2.98→3.11 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ABH

2abh


Resolution: 2.98→17.06 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.831 / SU B: 38.286 / SU ML: 0.364 / Cross valid method: THROUGHOUT / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24922 2333 5 %RANDOM
Rwork0.17423 ---
obs0.17804 44230 92.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.834 Å2
Baniso -1Baniso -2Baniso -3
1-27.22 Å20 Å2-34.96 Å2
2---25.65 Å20 Å2
3----1.56 Å2
Refinement stepCycle: LAST / Resolution: 2.98→17.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18677 0 170 28 18875
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0219281
X-RAY DIFFRACTIONr_bond_other_d0.0030.0218189
X-RAY DIFFRACTIONr_angle_refined_deg2.1731.95526278
X-RAY DIFFRACTIONr_angle_other_deg1.203341954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.02752497
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.69325.834725
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.234152945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1981516
X-RAY DIFFRACTIONr_chiral_restr0.1090.22872
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02122100
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024200
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_it1.1972.48310015
X-RAY DIFFRACTIONr_mcbond_other1.1962.48310014
X-RAY DIFFRACTIONr_mcangle_it2.0413.72212503
X-RAY DIFFRACTIONr_mcangle_other2.0413.72212504
X-RAY DIFFRACTIONr_scbond_it0.9592.5419266
X-RAY DIFFRACTIONr_scbond_other0.8992.5319131
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5923.77213572
X-RAY DIFFRACTIONr_long_range_B_refined5.67923.48281348
X-RAY DIFFRACTIONr_long_range_B_other5.67923.48281349
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.985→3.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 142 -
Rwork0.227 2615 -
obs--74.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.8244-0.0308-0.04281.1996-0.74060.6771-0.02260.0284-0.0454-0.1180.0240.0413-0.0938-0.2068-0.00140.32670.06660.16790.2043-0.09940.195852.137176.232163.322
20.36620.35860.14950.65620.13850.8992-0.0505-0.0373-0.026-0.08120.01760.05930.1440.00220.03290.3366-0.03340.17330.03990.00340.127173.748925.353865.4047
30.5044-0.18750.19861.0224-0.15240.58130.0563-0.03810.04770.0409-0.06370.0597-0.0007-0.10980.00730.1799-0.01340.19510.1939-0.0120.212752.780352.5097139.462
40.2662-0.08610.40750.84970.59691.5163-0.01710.11280.03310.06130.0841-0.1029-0.00990.111-0.06690.1708-0.01830.20040.1862-0.02110.278188.475948.5865131.6753
50.7158-0.10340.02440.76890.33581.04010.11570.0099-0.0197-0.0232-0.0615-0.02660.0456-0.0752-0.05420.1918-0.03770.17130.1280.01890.210547.825745.3707104.9113
60.80640.29550.10871.08030.03770.7017-0.06570.1386-0.127-0.01310.1295-0.1381-0.0555-0.0582-0.06380.1801-0.00760.1890.1303-0.03170.213976.913122.9131109.1841
70.5776-0.14730.0950.43480.06210.86690.04450.0739-0.04540.1677-0.03910.0463-0.1266-0.2095-0.00530.30650.04760.18760.1029-0.00840.170949.536985.432197.5855
82.02650.5139-0.0521.6015-0.54370.69520.078-0.06930.04850.0175-0.1054-0.0399-0.08080.09060.02740.351-0.05250.17270.0191-0.01840.091884.564151.6515176.9179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 340
2X-RAY DIFFRACTION2B27 - 340
3X-RAY DIFFRACTION3C27 - 339
4X-RAY DIFFRACTION4D27 - 340
5X-RAY DIFFRACTION5E27 - 340
6X-RAY DIFFRACTION6F27 - 340
7X-RAY DIFFRACTION7G27 - 340
8X-RAY DIFFRACTION8H27 - 336

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