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- PDB-1eks: ASP128ALA VARIANT OF MOAC PROTEIN FROM E. COLI -

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Basic information

Entry
Database: PDB / ID: 1eks
TitleASP128ALA VARIANT OF MOAC PROTEIN FROM E. COLI
ComponentsMOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN C
KeywordsTRANSLATION / MoaC / Molybdenum cofactor (Moco) / Moco biosynthesis / Moco deficiency
Function / homology
Function and homology information


cyclic pyranopterin monophosphate synthase / cyclic pyranopterin monophosphate synthase activity / Mo-molybdopterin cofactor biosynthetic process / protein-containing complex / identical protein binding
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
L(+)-TARTARIC ACID / Cyclic pyranopterin monophosphate synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.5 Å
AuthorsSchindelin, H. / Liu, M.T.W. / Wuebbens, M.M. / Rajagopalan, K.V.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Insights into molybdenum cofactor deficiency provided by the crystal structure of the molybdenum cofactor biosynthesis protein MoaC.
Authors: Wuebbens, M.M. / Liu, M.T. / Rajagopalan, K. / Schindelin, H.
History
DepositionMar 9, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5832
Polymers17,4331
Non-polymers1501
Water724
1
A: MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN C
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)105,50012
Polymers104,6006
Non-polymers9016
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation10_666-y+1,-x+1,-z+3/21
crystal symmetry operation11_656-x+y+1,y,-z+3/21
crystal symmetry operation12_556x,x-y,-z+3/21
Buried area19590 Å2
ΔGint-105 kcal/mol
Surface area31610 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.128, 92.128, 63.289
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
DetailsThe biological assembly is a hexamer with 32 symmetry generated from chain A by crystallographic symmetry operations

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Components

#1: Protein MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN C


Mass: 17433.268 Da / Num. of mol.: 1 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PET 15B / Cellular location (production host): CYTOSOL / Production host: Escherichia coli (E. coli) / References: UniProt: P0A738
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: Ammonium Phosphate, Sodium-Potassium Tartrate, Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 22K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.7-2.1 M1reservoirNH42HPO4
20.05-0.1 MK,Na tartrate1reservoir
30.1 Mcitrate1reservoir

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 23, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.48→20 Å / Num. all: 19808 / Num. obs: 5826 / % possible obs: 0.971 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 50.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 13
Reflection shellResolution: 2.48→2.59 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.516 / % possible all: 98.6
Reflection shell
*PLUS
% possible obs: 98.6 % / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.5→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Lamzin
Details: Partial structure factors for bulk solvent were calculated in XPLOR and incorporated into REFMAC
RfactorNum. reflectionSelection details
Rfree0.2759 567 Random
Rwork0.2171 --
all-5665 -
obs-5098 -
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1063 0 10 4 1077
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.008
X-RAY DIFFRACTIONp_angle_d0.03
X-RAY DIFFRACTIONplanar groups (peptides)0.016
X-RAY DIFFRACTIONplanar groups (aromatics)0.0067
X-RAY DIFFRACTIONchiral volumes0.109
X-RAY DIFFRACTIONtorsion angles (planar)3.3
X-RAY DIFFRACTIONtorsion angles (staggered)21.4
X-RAY DIFFRACTIONtorsion angles (orthonormal)26.1
X-RAY DIFFRACTIONB-factors (main chain bond)3
X-RAY DIFFRACTIONB-factors (main chain angle)4.84
X-RAY DIFFRACTIONB-factors (side chain bond)3.32
X-RAY DIFFRACTIONB-factors (side chain angle)5.4
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.276 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_planar_d0.042
X-RAY DIFFRACTIONp_chiral_restr0.109

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