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- PDB-2f1r: Crystal Structure of molybdopterin-guanine biosynthesis protein B... -

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Basic information

Entry
Database: PDB / ID: 2f1r
TitleCrystal Structure of molybdopterin-guanine biosynthesis protein B (mobB)
Componentsmolybdopterin-guanine dinucleotide biosynthesis protein B (mobB)
KeywordsBIOSYNTHETIC PROTEIN / Molybdopterin / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process / GTP binding
Similarity search - Function
Molybdopterin-guanine dinucleotide biosynthesis protein B (MobB) domain / Molybdopterin guanine dinucleotide synthesis protein B / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PRASEODYMIUM ION / Molybdopterin-guanine dinucleotide biosynthesis protein B (MobB)
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsDamodharan, L. / Eswaramoorthy, S. / Kumaran, D. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of molybdopterin-guanine dinucleotide biosynthesis protein B (mobB)
Authors: Damodharan, L. / Eswaramoorthy, S. / Kumaran, D. / Swaminathan, S.
History
DepositionNov 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details ..._audit_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 600HETEROGEN Praseodymium ion PR is hydrated by the water molecules 164-173.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: molybdopterin-guanine dinucleotide biosynthesis protein B (mobB)
B: molybdopterin-guanine dinucleotide biosynthesis protein B (mobB)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6514
Polymers39,4752
Non-polymers1762
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-34 kcal/mol
Surface area14160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.98, 63.93, 66.01
Angle α, β, γ (deg.)90.00, 95.3, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein molybdopterin-guanine dinucleotide biosynthesis protein B (mobB)


Mass: 19737.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Production host: Escherichia coli (E. coli) / References: UniProt: O28031
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PR / PRASEODYMIUM ION


Mass: 140.908 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pr
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 39.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.51
Details: 20% Peg 3350, 0.1M Bis-Tris, additive 0.1M Praseodymium (III) acetate, pH 5.51, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 6, 2005 / Details: Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 17059 / Num. obs: 17059 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.8 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 14.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.172 / Num. unique all: 798 / % possible all: 43.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CBASSdata collection
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.883 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.279 / ESU R Free: 0.226 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2534 1337 7.8 %RANDOM
Rwork0.1861 ---
all0.1912 15707 --
obs0.1912 15707 92.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20.84 Å2
2--0.31 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2390 0 2 166 2558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222438
X-RAY DIFFRACTIONr_angle_refined_deg1.8541.9813312
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5965289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80422.018114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.67515463
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7271531
X-RAY DIFFRACTIONr_chiral_restr0.1260.2372
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021783
X-RAY DIFFRACTIONr_nbd_refined0.2190.21047
X-RAY DIFFRACTIONr_nbtor_refined0.3070.21658
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2167
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.224
X-RAY DIFFRACTIONr_mcbond_it1.1421.51455
X-RAY DIFFRACTIONr_mcangle_it2.08722360
X-RAY DIFFRACTIONr_scbond_it3.2483983
X-RAY DIFFRACTIONr_scangle_it5.2344.5952
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 29 -
Rwork0.188 417 -
obs--32.84 %

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