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- PDB-3f2i: Crystal structure of the alr0221 protein from Nostoc, Northeast S... -

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Basic information

Entry
Database: PDB / ID: 3f2i
TitleCrystal structure of the alr0221 protein from Nostoc, Northeast Structural Genomics Consortium Target NsR422.
ComponentsAlr0221 protein
Keywordsstructural genomics / unknown function / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


protein histidine phosphatase activity / protein modification process / cytoplasm
Similarity search - Function
Phosphohistidine phosphatase SixA / : / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Alr0221 protein
Similarity search - Component
Biological speciesNostoc sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsForouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Belote, R.L. / Nair, R. / Everett, J.K. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Belote, R.L. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the alr0221 protein from Nostoc, Northeast Structural Genomics Consortium Target NsR422.
Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Foote, E.L. / Ciccosanti, C. / Belote, R.L. / Nair, R. / Everett, J.K. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionOct 29, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Alr0221 protein
B: Alr0221 protein
C: Alr0221 protein
D: Alr0221 protein
E: Alr0221 protein
F: Alr0221 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,93318
Polymers119,1516
Non-polymers78312
Water7,404411
1
A: Alr0221 protein
B: Alr0221 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9786
Polymers39,7172
Non-polymers2614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3150 Å2
ΔGint-47 kcal/mol
Surface area14430 Å2
MethodPISA
2
C: Alr0221 protein
D: Alr0221 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9786
Polymers39,7172
Non-polymers2614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3110 Å2
ΔGint-49 kcal/mol
Surface area14510 Å2
MethodPISA
3
E: Alr0221 protein
F: Alr0221 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9786
Polymers39,7172
Non-polymers2614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-47 kcal/mol
Surface area14800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.099, 94.329, 92.062
Angle α, β, γ (deg.)90.00, 93.64, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Alr0221 protein


Mass: 19858.457 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nostoc sp. (bacteria) / Strain: PCC 7120 / Gene: alr0221 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q8Z077
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / 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: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 277 K / pH: 8
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM TRIS (pH 8), 20% PEG 8K, and 100 mM NH4H2PO4, microbatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 17, 2008 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 150244 / Num. obs: 148291 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 6.3 Å2 / Rmerge(I) obs: 0.088 / Rsym value: 0.069 / Net I/σ(I): 15.6
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.345 / Mean I/σ(I) obs: 2.95 / Num. unique all: 15001 / Rsym value: 0.303 / % possible all: 90

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXthen SOLVE/RESOLVEmodel building
CNS1.2 & XtalViewrefinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXthen SOLVE/RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.93 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 298906.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.24 6303 5 %RANDOM
Rwork0.196 ---
all0.197 147681 --
obs0.196 126268 85.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.8533 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 23 Å2
Baniso -1Baniso -2Baniso -3
1--3.96 Å20 Å21.2 Å2
2--6.53 Å20 Å2
3----2.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7883 0 36 411 8330
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.277 494 5.1 %
Rwork0.208 9199 -
obs-9199 65.9 %

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