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- PDB-2ph1: Crystal structure of nucleotide-binding protein AF2382 from Archa... -

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Basic information

Entry
Database: PDB / ID: 2ph1
TitleCrystal structure of nucleotide-binding protein AF2382 from Archaeoglobus fulgidus, Northeast Structural Genomics Target GR165
ComponentsNucleotide-binding protein
KeywordsLIGAND BINDING PROTEIN / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


iron-sulfur cluster binding / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Mrp/NBP35 ATP-binding protein / Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 / NUBPL iron-transfer P-loop NTPase / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Iron-sulfur cluster carrier protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsForouhar, F. / Abashidze, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. ...Forouhar, F. / Abashidze, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of nucleotide-binding protein AF2382 from Archaeoglobus fulgidus.
Authors: Forouhar, F. / Abashidze, M. / Seetharaman, J. / Janjua, H. / Fang, Y. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionApr 10, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 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
A: Nucleotide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3392
Polymers29,2741
Non-polymers651
Water66737
1
A: Nucleotide-binding protein
hetero molecules

A: Nucleotide-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6784
Polymers58,5472
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area1500 Å2
ΔGint-73 kcal/mol
Surface area22390 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.937, 78.186, 49.597
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-301-

ZN

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Components

#1: Protein Nucleotide-binding protein


Mass: 29273.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Species: Archaeoglobus fulgidus / Strain: DSM 4304, VC-16, JCM 9628, NBRC 100126 / Gene: AF_2382 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: O30288
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 44.49 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS
Crystal growTemperature: 293 K / Method: microbatch under oil / pH: 7.5
Details: Protein solution: 20 mM Tris-HCl pH 7.5, 100 mM Sodium chloride, 5 mM DTT. Precipitant solution: 100 mM HEPES pH 7.5, 55% MPD, MICROBATCH UNDER OIL, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 27, 2007 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→49.6 Å / Num. all: 13903 / Num. obs: 13903 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 35.1 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.079 / Net I/σ(I): 18.54
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 5.08 / Num. unique all: 1539 / Rsym value: 0.344 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→49.6 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 112851.27 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: XtalView has also been used in the refinement. THE FRIEDEL PAIRS WERE USED FOR PHASING
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1211 9.7 %RANDOM
Rwork0.217 ---
all0.218 13903 --
obs0.217 12442 90.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 24.7637 Å2 / ksol: 0.296708 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1--15.84 Å20 Å20 Å2
2--14.77 Å20 Å2
3---1.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.7→49.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1898 0 1 37 1936
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.8 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.357 104 9.9 %
Rwork0.271 948 -
obs-948 76.4 %

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