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- PDB-2eey: Structure of GK0241 protein from Geobacillus kaustophilus -

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Basic information

Entry
Database: PDB / ID: 2eey
TitleStructure of GK0241 protein from Geobacillus kaustophilus
ComponentsMolybdopterin biosynthesis
KeywordsBIOSYNTHETIC PROTEIN / Molybdenium precursor bosynthesis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


cyclic pyranopterin monophosphate synthase / cyclic pyranopterin monophosphate synthase activity / Mo-molybdopterin cofactor biosynthetic process
Similarity search - Function
: / Molybdopterin cofactor biosynthesis C (MoaC) domain / Molybdopterin cofactor biosynthesis C (MoaC) domain / Molybdenum cofactor biosynthesis C / Molybdopterin cofactor biosynthesis C (MoaC) domain superfamily / MoaC family / : / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Cyclic pyranopterin monophosphate synthase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsLokanath, N.K. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure of GK0241 protein from Geobacillus kaustophilus
Authors: Lokanath, N.K. / Pampa, K.J. / Kamiya, N. / Kunishima, N.
History
DepositionFeb 19, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdopterin biosynthesis


Theoretical massNumber of molelcules
Total (without water)17,4921
Polymers17,4921
Non-polymers00
Water2,306128
1
A: Molybdopterin biosynthesis
x 6


Theoretical massNumber of molelcules
Total (without water)104,9546
Polymers104,9546
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_445z-1/2,-x-1/2,-y1
crystal symmetry operation12_455-y-1/2,-z,x+1/21
crystal symmetry operation13_455y-1/4,x+1/4,-z+1/41
crystal symmetry operation18_445-x-3/4,z-1/4,y+1/41
crystal symmetry operation24_444-z-1/4,-y-1/4,-x-1/41
Buried area25010 Å2
ΔGint-189 kcal/mol
Surface area34180 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)105.240, 105.240, 105.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-166-

HOH

21A-270-

HOH

31A-276-

HOH

41A-281-

HOH

51A-289-

HOH

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Components

#1: Protein Molybdopterin biosynthesis / Molybdenum cofactor biosynthesis protein C


Mass: 17492.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Plasmid: pET-HisTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q5L3F4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.9
Details: 0.12M Citrate-HCl, 0.25M Na formate, 0.1M NH(2)SO(4) and 22% PEG 4K, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 4, 2006 / Details: GRAPHITE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. all: 15364 / Num. obs: 15314 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 40 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.9
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 39 % / Rmerge(I) obs: 0.424 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EKR

1ekr


Resolution: 1.94→37.21 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 4192177.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.192 759 5 %RANDOM
Rwork0.191 ---
obs0.191 15314 99.8 %-
all-15364 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.4936 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.94→37.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1200 0 0 128 1328
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.5
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 1.94→2.06 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.221 136 5.5 %
Rwork0.201 2337 -
obs--99.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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