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- PDB-1sum: Crystal structure of a hypothetical protein at 2.0 A resolution -

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Basic information

Entry
Database: PDB / ID: 1sum
TitleCrystal structure of a hypothetical protein at 2.0 A resolution
ComponentsPhosphate transport system protein phoU homolog 2
KeywordsTRANSPORT PROTEIN / PhoU / ABC transport / pst / Structural Genomics / Berkeley Structural Genomics Center / BSGC / structure funded by NIH / Protein Structure Initiative / PSI
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 / 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
: / NICKEL (II) ION / PHOSPHITE ION / Phosphate-specific transport system accessory protein PhoU homolog 2
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsLiu, J. / Lou, Y. / Yokota, H. / Adams, P.D. / Kim, R. / Kim, S.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of a PhoU protein homologue: a new class of metalloprotein containing multinuclear iron clusters.
Authors: Liu, J. / Lou, Y. / Yokota, H. / Adams, P.D. / Kim, R. / Kim, S.H.
History
DepositionMar 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Phosphate transport system protein phoU homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,49912
Polymers26,8511
Non-polymers64811
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphate transport system protein phoU homolog 2
hetero molecules

B: Phosphate transport system protein phoU homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,99824
Polymers53,7022
Non-polymers1,29522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7500 Å2
ΔGint-227 kcal/mol
Surface area18710 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.677, 90.677, 45.255
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules B

#1: Protein Phosphate transport system protein phoU homolog 2


Mass: 26851.193 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: pB4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pSJS1244 Star / References: UniProt: Q9X256

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Non-polymers , 5 types, 89 molecules

#2: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-PO3 / PHOSPHITE ION / Phosphite ester


Mass: 78.972 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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 Å3/Da / Density % sol: 38.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 50mM Hepes, 100mM CaCl2, 25% PEG 400, pH 7.0, 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: 0.9796, 0.9798, 0.9600
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 22, 2003
RadiationMonochromator: Yale MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97981
30.961
ReflectionResolution: 2→20 Å / Num. all: 14730 / Num. obs: 14583 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.05 Å / % possible all: 96

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHENIXmodel building
REFMAC5.1refinement
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.944 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25489 1205 8.3 %RANDOM
Rwork0.2166 ---
obs0.21993 13369 98.95 %-
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: 19.892 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å2-0.99 Å20 Å2
2---1.98 Å20 Å2
3---2.97 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 17 78 1898
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221836
X-RAY DIFFRACTIONr_bond_other_d0.0020.021735
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9962470
X-RAY DIFFRACTIONr_angle_other_deg0.77334055
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3625224
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_restr0.0710.2285
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021978
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02330
X-RAY DIFFRACTIONr_nbd_refined0.2060.2495
X-RAY DIFFRACTIONr_nbd_other0.2220.22029
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.21125
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.248
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1520.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2280.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4990.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7341.51124
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.35121820
X-RAY DIFFRACTIONr_scbond_it2.2253712
X-RAY DIFFRACTIONr_scangle_it3.7424.5650
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.001→2.052 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.325 76
Rwork0.228 931
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)
14.99563.784-0.48267.9526-0.32241.1340.3172-0.52430.67010.5548-0.31910.5441-0.2101-0.02160.00190.24320.03570.06020.2468-0.08880.137618.80645.25749.83
26.29344.50071.16198.58040.96281.62110.3024-0.515-0.48690.7144-0.3077-0.37990.12030.03160.00530.21950.033-0.01340.24660.06580.02421.852227.079210.8854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1BA2 - 1082 - 108
2X-RAY DIFFRACTION2BA117 - 208117 - 208

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