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- PDB-4fdf: Structural insights into putative molybdenum cofactor biosynthesi... -

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Basic information

Entry
Database: PDB / ID: 4fdf
TitleStructural insights into putative molybdenum cofactor biosynthesis protein C (MoaC2) from Mycobacterium tuberculosis H37Rv
ComponentsMolybdenum cofactor biosynthesis protein C 2
KeywordsBIOSYNTHETIC PROTEIN / MoaC2 / Ferrodoxin-like fold / Moco biosynthesis
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 2 / Cyclic pyranopterin monophosphate synthase 2
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsSrivastava, V.K. / Srivastava, S. / Arora, A. / Pratap, J.V.
CitationJournal: Plos One / Year: 2013
Title: Structural Insights into Putative Molybdenum Cofactor Biosynthesis Protein C (MoaC2) from Mycobacterium tuberculosis H37Rv.
Authors: Srivastava, V.K. / Srivastava, S. / Arora, A. / Pratap, J.V.
History
DepositionMay 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdenum cofactor biosynthesis protein C 2
B: Molybdenum cofactor biosynthesis protein C 2


Theoretical massNumber of molelcules
Total (without water)37,3872
Polymers37,3872
Non-polymers00
Water1,17165
1
A: Molybdenum cofactor biosynthesis protein C 2
B: Molybdenum cofactor biosynthesis protein C 2

A: Molybdenum cofactor biosynthesis protein C 2
B: Molybdenum cofactor biosynthesis protein C 2

A: Molybdenum cofactor biosynthesis protein C 2
B: Molybdenum cofactor biosynthesis protein C 2


Theoretical massNumber of molelcules
Total (without water)112,1606
Polymers112,1606
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area18290 Å2
ΔGint-104 kcal/mol
Surface area25650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.900, 91.900, 91.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein Molybdenum cofactor biosynthesis protein C 2


Mass: 18693.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: M. tuberculosis, moaC2, MT0887, MTV043.57, Rv0864 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P0A5K6, UniProt: P9WJR7*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 1.73 Å3/Da / Density % sol: 28.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.025M potassium sodium tartrate tetra hydrate solution, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.976 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.2→27.71 Å / Num. obs: 13345 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.2→2.28 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.6.0111refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EKR

1ekr


Resolution: 2.202→27.71 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.773 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24942 647 4.9 %RANDOM
Rwork0.20546 ---
obs0.2075 12651 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.449 Å2
Refinement stepCycle: LAST / Resolution: 2.202→27.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 0 65 1982
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221934
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1161.9742637
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.675268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.15223.57156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.60615306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.3221513
X-RAY DIFFRACTIONr_chiral_restr0.0720.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211371
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 48 -
Rwork0.278 841 -
obs--99.78 %

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