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- PDB-1g8l: CRYSTAL STRUCTURE OF ESCHERICHIA COLI MOEA -

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Basic information

Entry
Database: PDB / ID: 1g8l
TitleCRYSTAL STRUCTURE OF ESCHERICHIA COLI MOEA
ComponentsMOLYBDOPTERIN BIOSYNTHESIS MOEA PROTEIN
KeywordsMETAL BINDING PROTEIN / Molybdenum cofactor biosynthesis
Function / homology
Function and homology information


molybdopterin molybdotransferase / molybdopterin molybdotransferase activity / Mo-molybdopterin cofactor biosynthetic process / protein homodimerization activity / identical protein binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdenum cofactor biosynthesis proteins signature 2. / Molybdopterin biosynthesis moea protein, domain 2 / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily ...Molybdopterin biosynthesis moeA protein; domain 3 / Molybdopterin biosynthesis moea protein, domain 3. / Beta-clip / MoeA, C-terminal, domain IV / Molybdenum cofactor biosynthesis proteins signature 2. / Molybdopterin biosynthesis moea protein, domain 2 / MoeA, N-terminal and linker domain / MoeA, C-terminal, domain IV / MoeA, N-terminal and linker domain superfamily / MoeA, C-terminal, domain IV superfamily / Molybdopterin biosynthesis protein MoeA-like / MoeA N-terminal region (domain I and II) / MoeA C-terminal region (domain IV) / Molybdopterin biosynthesis moea protein, domain 2 / 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 / Beta Complex / Alpha-Beta Complex / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Molybdopterin molybdenumtransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.95 Å
AuthorsXiang, S. / Nichols, J. / Rajagopalan, K.V. / Schindelin, H.
CitationJournal: Structure / Year: 2001
Title: The crystal structure of Escherichia coli MoeA and its relationship to the multifunctional protein gephyrin.
Authors: Xiang, S. / Nichols, J. / Rajagopalan, K.V. / Schindelin, H.
History
DepositionNov 17, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MOLYBDOPTERIN BIOSYNTHESIS MOEA PROTEIN
B: MOLYBDOPTERIN BIOSYNTHESIS MOEA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,87020
Polymers88,2122
Non-polymers1,65818
Water10,683593
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8520 Å2
ΔGint-34 kcal/mol
Surface area33700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.323, 97.414, 98.739
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein MOLYBDOPTERIN BIOSYNTHESIS MOEA PROTEIN


Mass: 44106.059 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: P12281
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 593 / 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: 5

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4148.88
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop6.5PEG 8000, calcium acetate, cacodylaic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
2982vapor diffusion, hanging drop6.5PEG 6000, calcium acetate, cacodylaic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-15 %PEG60001reservoiror PEG8000
20.2-0.5 Mcalcium acetate1reservoir
30.1 Mcacodylic acid1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
22
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X26C11.1
SYNCHROTRONNSLS X12B20.98
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDNov 1, 1999
ADSC QUANTUM 42CCDJan 1, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
20.981
ReflectionResolution: 1.9→50 Å / Num. all: 66845 / Num. obs: 66845 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 27.064 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 12.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.15 % / Rmerge(I) obs: 0.674 / Mean I/σ(I) obs: 1.25 / Num. unique all: 6542 / Rsym value: 0.674 / % possible all: 98.9
Reflection
*PLUS
Highest resolution: 2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.069
Reflection shell
*PLUS
% possible obs: 99.2 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameClassification
SHARPphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR
Starting model: None

Resolution: 1.95→20 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.284 2892 -random
Rwork0.228 ---
all0.23 54423 --
obs0.23 54423 91.5 %-
Displacement parametersBiso mean: 26.205 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å20 Å2
2---0.96 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6080 0 108 593 6781
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.379
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_mcbond_it2.113
X-RAY DIFFRACTIONx_mcangle_it3.214
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 50 Å / Num. reflection obs: 51382 / Rfactor Rfree: 0.277 / Rfactor Rwork: 0.209
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.022
X-RAY DIFFRACTIONx_angle_deg1.609
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.56
X-RAY DIFFRACTIONx_plane_restr0.007
X-RAY DIFFRACTIONx_chiral_restr0.116

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