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- PDB-3ngw: Crystal Structure of Molybdopterin-guanine dinucleotide biosynthe... -

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Basic information

Entry
Database: PDB / ID: 3ngw
TitleCrystal Structure of Molybdopterin-guanine dinucleotide biosynthesis protein A from Archaeoglobus fulgidus, Northeast Structural Genomics Consortium Target GR189
ComponentsMolybdopterin-guanine dinucleotide biosynthesis protein A (MobA)
KeywordsBIOSYNTHETIC PROTEIN / alpha-beta protein / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process / catalytic activity / GTP binding / metal ion binding
Similarity search - Function
Molybdenum cofactor guanylyltransferase / MobA-like NTP transferase / MobA-like NTP transferase domain / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Molybdopterin-guanine dinucleotide biosynthesis protein A (MobA)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target GR189
Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdopterin-guanine dinucleotide biosynthesis protein A (MobA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0953
Polymers24,0151
Non-polymers802
Water1,04558
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Molybdopterin-guanine dinucleotide biosynthesis protein A (MobA)
hetero molecules

A: Molybdopterin-guanine dinucleotide biosynthesis protein A (MobA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1916
Polymers48,0302
Non-polymers1604
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_566x,-y+1,-z+3/21
Buried area2840 Å2
ΔGint-28 kcal/mol
Surface area17120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.100, 116.100, 116.100
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-210-

CA

DetailsThe current crystal structure reveals that the protein forms dimer, whereas the static light scattering data suggests that it forms monomer in the solution.

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Components

#1: Protein Molybdopterin-guanine dinucleotide biosynthesis protein A (MobA)


Mass: 24015.121 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Strain: DSM 4304 / Gene: AF_2005, mobA / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: O28274
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 2.72 Å3/Da / Density % sol: 54.7 %
Crystal growTemperature: 277 K / pH: 7
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M Bis-Tris Propane (pH 7), 20% (W/V) PEG 8k, 0.1M calcium chloride dihydrate, and 20% ...Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M Bis-Tris Propane (pH 7), 20% (W/V) PEG 8k, 0.1M calcium chloride dihydrate, and 20% ethylene glycol as the cryo-protectant, Microbatch, under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97908 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 22242 / Num. obs: 21953 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 26.8 Å2 / Rmerge(I) obs: 0.093 / Rsym value: 0.067 / Net I/σ(I): 20.05
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 2.96 / Num. unique all: 2218 / Rsym value: 0.433 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
SnBfollowed by SOLVE/RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.31→19.91 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 365342.156 / 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
Rfree0.226 1757 9.4 %RANDOM
Rwork0.183 ---
all0.192 22240 --
obs0.187 18771 84.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.634 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 44.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.31→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1559 0 2 58 1619
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 2.3→2.38 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.252 126 9.4 %
Rwork0.209 1211 -
obs-1337 58.4 %

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