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- PDB-3l39: Crystal structure of Putative PhoU-like phosphate regulatory prot... -

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Basic information

Entry
Database: PDB / ID: 3l39
TitleCrystal structure of Putative PhoU-like phosphate regulatory protein (BT4638) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.93 A resolution
ComponentsPutative PhoU-like phosphate regulatory protein
Keywordsphosphate-binding protein / BT4638 / Putative PhoU-like phosphate regulatory protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


: / Putative phosphate transport regulator / Protein of unknown function DUF47 / 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 ION / DUF47 domain-containing protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.93 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative PhoU-like phosphate regulatory protein (BT4638) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.93 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative PhoU-like phosphate regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1648
Polymers26,4991
Non-polymers6657
Water3,369187
1
A: Putative PhoU-like phosphate regulatory protein
hetero molecules

A: Putative PhoU-like phosphate regulatory protein
hetero molecules

A: Putative PhoU-like phosphate regulatory protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,49224
Polymers79,4983
Non-polymers1,99421
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area8900 Å2
ΔGint-159 kcal/mol
Surface area26560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.587, 79.587, 237.385
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-243-

HOH

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Components

#1: Protein Putative PhoU-like phosphate regulatory protein


Mass: 26499.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT4638, BT_4638 / Plasmid: MH4a / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q89YU3
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHH FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.73 Å3/Da / Density % sol: 54.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20.0% Glycerol, 1.6M NH4H2PO3, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979245
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 18, 2004 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979245 Å / Relative weight: 1
ReflectionResolution: 1.93→44.972 Å / Num. obs: 18980 / % possible obs: 85.3 % / Redundancy: 5.3 % / Biso Wilson estimate: 16.512 Å2 / Rsym value: 0.071

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
MolProbity3beta29model building
SCALA3.3.15data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2iiu,1xwm

2iiu

1xwm


Resolution: 1.93→44.972 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.934 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 2.679 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. PHOSPHATES (PO4) FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 981 5.2 %RANDOM
Rwork0.166 ---
obs0.168 18940 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 63.46 Å2 / Biso mean: 14.477 Å2 / Biso min: 3.05 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.16 Å20 Å2
2--0.33 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.93→44.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1786 0 35 187 2008
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221867
X-RAY DIFFRACTIONr_bond_other_d0.0010.021262
X-RAY DIFFRACTIONr_angle_refined_deg1.4712.0052562
X-RAY DIFFRACTIONr_angle_other_deg0.9833140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0755249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17425.49591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.8415360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.928159
X-RAY DIFFRACTIONr_chiral_restr0.0980.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212063
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02342
X-RAY DIFFRACTIONr_mcbond_it0.86921115
X-RAY DIFFRACTIONr_mcbond_other0.162435
X-RAY DIFFRACTIONr_mcangle_it1.52631841
X-RAY DIFFRACTIONr_scbond_it1.0682752
X-RAY DIFFRACTIONr_scangle_it1.843699
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.368 32 -
Rwork0.296 496 -
all-528 -
obs--100 %

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