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- PDB-1y5e: Crystal structure of Molybdenum cofactor biosynthesis protein B -

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Basic information

Entry
Database: PDB / ID: 1y5e
TitleCrystal structure of Molybdenum cofactor biosynthesis protein B
ComponentsMolybdenum cofactor biosynthesis protein B
KeywordsBIOSYNTHETIC PROTEIN / Structural Genomics / Protein Structure Initiative / PSI / MCSG / Midwest Center for Structural Genomics / Molybdenum cofactor biosynthesis
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process / cytosol
Similarity search - Function
Molybdenum cofactor biosynthesis protein MoaB / Molybdenum cofactor biosynthesis proteins signature 1. / Molybdenum cofactor biosynthesis, conserved site / MoaB/Mog-like domain / Molybdenum Cofactor Biosythetic Enzyme; Chain A / MoaB/Mog domain / MoaB/Mog-like domain superfamily / Probable molybdopterin binding domain / Probable molybdopterin binding domain / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / Molybdenum cofactor biosynthesis protein B
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsChang, C. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of Molybdenum cofactor biosynthesis protein B
Authors: Chang, C. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionDec 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Molybdenum cofactor biosynthesis protein B
B: Molybdenum cofactor biosynthesis protein B
C: Molybdenum cofactor biosynthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4405
Polymers56,2533
Non-polymers1872
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5390 Å2
ΔGint-37 kcal/mol
Surface area20320 Å2
MethodPISA
2
A: Molybdenum cofactor biosynthesis protein B
B: Molybdenum cofactor biosynthesis protein B
C: Molybdenum cofactor biosynthesis protein B
hetero molecules

A: Molybdenum cofactor biosynthesis protein B
B: Molybdenum cofactor biosynthesis protein B
C: Molybdenum cofactor biosynthesis protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,88010
Polymers112,5066
Non-polymers3754
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area13960 Å2
ΔGint-87 kcal/mol
Surface area37460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.952, 122.952, 74.536
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Molybdenum cofactor biosynthesis protein B


Mass: 18750.936 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: moaB / Plasmid: PMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q816R0
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.9 Å3/Da / Density % sol: 57.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: MPD, imidazole, MgCl2, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97943 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 4, 2004
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 99009 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.1 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 18.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.762 / Mean I/σ(I) obs: 1.744 / Num. unique all: 5095 / % possible all: 94.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→47.43 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 366315.55 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.215 8899 9.9 %RANDOM
Rwork0.188 ---
obs0.188 90222 90.7 %-
all-99472 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 52.6318 Å2 / ksol: 0.337812 e/Å3
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.1 Å2-0.37 Å20 Å2
2---2.1 Å20 Å2
3---4.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→47.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3649 0 5 445 4099
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.241.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it2.62
X-RAY DIFFRACTIONc_scangle_it3.822.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.282 1225 9.7 %
Rwork0.267 11420 -
obs--76.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3IMD_XPLOR_PAR.IMD_XPLOR_TOP.
X-RAY DIFFRACTION4MPD_XPLOR_PAR.TXTMPD_XPLOR_TOP.TXT

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