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- PDB-1t8b: Crystal structure of refolded PHOU-like protein (gi 2983430) from... -

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Basic information

Entry
Database: PDB / ID: 1t8b
TitleCrystal structure of refolded PHOU-like protein (gi 2983430) from Aquifex aeolicus
ComponentsPhosphate transport system protein phoU homolog
KeywordsTRANSPORT PROTEIN / alpha-helical protein consisting of two 3-helix bundles / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


negative regulation of phosphate transmembrane transport / negative regulation of phosphate metabolic process / phosphate ion transport / intracellular phosphate ion homeostasis / negative regulation of gene expression / protein homodimerization activity / cytoplasm
Similarity search - Function
Phosphate transport system protein PhoU / PhoU domain / PhoU domain / Phosphate transport system protein phou homolog 2; domain 2 / PhoU-like domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phosphate-specific transport system accessory protein PhoU homolog
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, molecular replacement / Resolution: 3.23 Å
AuthorsOganesyan, V. / Kim, S.-H. / Oganesyan, N. / Jancarik, J. / Adams, P.D. / Kim, R. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.Bacteriol. / Year: 2005
Title: Crystal structure of the "PhoU-like" phosphate uptake regulator from Aquifex aeolicus.
Authors: Oganesyan, V. / Oganesyan, N. / Adams, P.D. / Jancarik, J. / Yokota, H.A. / Kim, R. / Kim, S.H.
History
DepositionMay 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphate transport system protein phoU homolog
B: Phosphate transport system protein phoU homolog


Theoretical massNumber of molelcules
Total (without water)51,8902
Polymers51,8902
Non-polymers00
Water00
1
A: Phosphate transport system protein phoU homolog


Theoretical massNumber of molelcules
Total (without water)25,9451
Polymers25,9451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Phosphate transport system protein phoU homolog


Theoretical massNumber of molelcules
Total (without water)25,9451
Polymers25,9451
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
A: Phosphate transport system protein phoU homolog

B: Phosphate transport system protein phoU homolog


Theoretical massNumber of molelcules
Total (without water)51,8902
Polymers51,8902
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_654-y+1,x-y,z-1/31
Buried area3090 Å2
ΔGint-16 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.094, 85.094, 62.825
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 7 - 214 / Label seq-ID: 7 - 214

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsBiological assembly is monomeric

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Components

#1: Protein Phosphate transport system protein phoU homolog


Mass: 25944.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: PHOU, AQ_906 / Plasmid: pB4.1105B / Species (production host): Escherichia coli / Production host: Escherichia coli K12 (bacteria) / Strain (production host): K12 / References: UniProt: O67053

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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: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Lithium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 10, 2004 / Details: double Si(111) crystal
RadiationMonochromator: double Si(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.23→48 Å / Num. obs: 8109 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Biso Wilson estimate: 120 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 14
Reflection shellResolution: 3.23→3.393 Å / Redundancy: 2 % / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.78 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
Blu-Icedata collection
SCALEPACKdata scaling
MOLREPphasing
SOLVEphasing
PHENIXphasing
RefinementMethod to determine structure: SAD, molecular replacement
Starting model: pdb entry 1T72

1t72


Resolution: 3.23→15 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.94 / SU B: 33.07 / SU ML: 0.532 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R Free: 0.541 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: Matrix scaling, diagonal term 0.02
RfactorNum. reflection% reflectionSelection details
Rfree0.24846 367 4.6 %RANDOM
Rwork0.21427 ---
obs0.21596 7667 99.09 %-
all-8109 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 128.948 Å2
Baniso -1Baniso -2Baniso -3
1--3.79 Å2-1.89 Å20 Å2
2---3.79 Å20 Å2
3---5.68 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.532 Å0.541 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 3.23→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3358 0 0 0 3358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223396
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9824572
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8055414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2530
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022494
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.260.21869
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2128
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3740.26
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3181.52078
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.70523366
X-RAY DIFFRACTIONr_scbond_it1.39531318
X-RAY DIFFRACTIONr_scangle_it2.6124.51206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1679 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.030.05
tight thermal0.050.5
LS refinement shellResolution: 3.23→3.393 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.385 47
Rwork0.365 1037
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)
116.6352-6.22060.781914.3329-2.24423.8774-1.81520.86960.1078-0.25410.51310.06970.3561-0.31521.30210.374-0.2743-0.23660.2560.07660.32113.9785.8180.147
219.7933-5.5181.50029.44550.97474.3883-0.26660.51930.12031.5935-0.6847-0.19080.3347-0.07840.95130.5704-0.2153-0.15150.1420.13960.312140.62139.55929.471
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 2147 - 214
2X-RAY DIFFRACTION2BB7 - 2147 - 214

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