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- PDB-1g8r: MOEA -

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Basic information

Entry
Database: PDB / ID: 1g8r
TitleMOEA
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 / metal ion binding / identical protein 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 / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 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 / Molybdopterin biosynthesis moea protein, domain 2 / Molybdenum cofactor biosynthesis proteins signature 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 / MOLECULAR REPLACEMENT / Resolution: 2.65 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 20, 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 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)89,31714
Polymers88,2122
Non-polymers1,10512
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7750 Å2
ΔGint-29 kcal/mol
Surface area33530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.9, 98.6, 159.4
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.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
13.0759.9
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop6.5PEG 6000, calcium acetate, cacodylaic acid, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
2982vapor diffusion, hanging drop6.5PEG 8000, 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

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 30, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 34006 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.61 % / Biso Wilson estimate: 54.85 Å2 / Rmerge(I) obs: 0.101 / Rsym value: 0.101 / Net I/σ(I): 10.7
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.26 % / Rmerge(I) obs: 0.389 / Mean I/σ(I) obs: 1.39 / Num. unique all: 3148 / Rsym value: 0.389 / % possible all: 92.6
Reflection
*PLUS
Highest resolution: 2.7 Å / % possible obs: 98.8 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.098
Reflection shell
*PLUS
% possible obs: 98.6 % / Rmerge(I) obs: 0.309 / Mean I/σ(I) obs: 2.7

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Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G8L

1g8l


Resolution: 2.65→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2712 1622 -RANDOM
Rwork0.2206 ---
all-32318 --
obs-31921 98.8 %-
Displacement parametersBiso mean: 47.163 Å2
Baniso -1Baniso -2Baniso -3
1--22.484 Å20 Å20 Å2
2--17.901 Å20 Å2
3---4.583 Å2
Refinement stepCycle: LAST / Resolution: 2.65→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6080 0 72 206 6358
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.7 Å / Rfactor Rfree: 0.266 / Rfactor Rwork: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.478
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.91
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_plane_restr0.005
X-RAY DIFFRACTIONx_chiral_restr0.1
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scangle_it

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