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- PDB-1jwb: Structure of the Covalent Acyl-Adenylate Form of the MoeB-MoaD Pr... -

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Basic information

Entry
Database: PDB / ID: 1jwb
TitleStructure of the Covalent Acyl-Adenylate Form of the MoeB-MoaD Protein Complex
Components(MOLYBDOPTERIN ...) x 2
KeywordsLIGASE / MoeB: modified Rossmann fold / (2) Cys-X-X-Cys Zinc-binding motifs / MoaD: ubiquitin-like fold
Function / homology
Function and homology information


molybdopterin-synthase adenylyltransferase / molybdopterin-synthase adenylyltransferase activity / molybdopterin synthase complex / molybdopterin adenylyltransferase complex / ubiquitin-like modifier activating enzyme activity / sulfotransferase activity / thiosulfate-cyanide sulfurtransferase activity / Mo-molybdopterin cofactor biosynthetic process / nucleotidyltransferase activity / nucleotide binding ... molybdopterin-synthase adenylyltransferase / molybdopterin-synthase adenylyltransferase activity / molybdopterin synthase complex / molybdopterin adenylyltransferase complex / ubiquitin-like modifier activating enzyme activity / sulfotransferase activity / thiosulfate-cyanide sulfurtransferase activity / Mo-molybdopterin cofactor biosynthetic process / nucleotidyltransferase activity / nucleotide binding / protein homodimerization activity / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Molybdopterin synthase sulfurylase MoeB / Molybdopterin synthase sulfur carrier subunit / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Beta-grasp domain ...Molybdopterin synthase sulfurylase MoeB / Molybdopterin synthase sulfur carrier subunit / Sulfur carrier ThiS/MoaD-like / ThiS family / Molybdopterin synthase/thiamin biosynthesis sulphur carrier, beta-grasp / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Beta-grasp domain / Beta-grasp domain superfamily / Ubiquitin-like (UB roll) / NAD(P)-binding Rossmann-like Domain / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE MONOPHOSPHATE / Molybdopterin-synthase adenylyltransferase / Molybdopterin synthase sulfur carrier subunit
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsLake, M.W. / Wuebbens, M.M. / Rajagopalan, K.V. / Schindelin, H.
CitationJournal: Nature / Year: 2001
Title: Mechanism of ubiquitin activation revealed by the structure of a bacterial MoeB-MoaD complex.
Authors: Lake, M.W. / Wuebbens, M.M. / Rajagopalan, K.V. / Schindelin, H.
History
DepositionSep 3, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _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
B: MOLYBDOPTERIN BIOSYNTHESIS MOEB PROTEIN
D: MOLYBDOPTERIN [MPT] CONVERTING FACTOR, SUBUNIT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0155
Polymers35,5072
Non-polymers5093
Water2,414134
1
B: MOLYBDOPTERIN BIOSYNTHESIS MOEB PROTEIN
D: MOLYBDOPTERIN [MPT] CONVERTING FACTOR, SUBUNIT 1
hetero molecules

B: MOLYBDOPTERIN BIOSYNTHESIS MOEB PROTEIN
D: MOLYBDOPTERIN [MPT] CONVERTING FACTOR, SUBUNIT 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,03110
Polymers71,0134
Non-polymers1,0176
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area11780 Å2
ΔGint-108 kcal/mol
Surface area21350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.230, 77.230, 100.545
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe asymmetric unit contains a heterodimer comprised of (1) molecule of MoeB and (1) molecule of MoaD. The heterotetramer is generated by applying: -y+1,-x+1,1/2-z

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Components

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MOLYBDOPTERIN ... , 2 types, 2 molecules BD

#1: Protein MOLYBDOPTERIN BIOSYNTHESIS MOEB PROTEIN


Mass: 26741.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MoeB / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P12282
#2: Protein MOLYBDOPTERIN [MPT] CONVERTING FACTOR, SUBUNIT 1 / MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN D


Mass: 8764.880 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: MoaD / Plasmid: pET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P30748

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Non-polymers , 4 types, 137 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.11 Å3/Da / Density % sol: 41.72 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Lithium Sulfate, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
123 mg/mlMoeB1drop
210 mg/mlMoaD1drop
31.7 M1reservoirLi2SO4
4100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 14, 2000
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 18549 / Num. obs: 18549 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 8.6
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 1.3 / % possible all: 98.1
Reflection
*PLUS

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: REFMAC Dictionary
RfactorNum. reflection% reflectionSelection details
Rfree0.22494 773 4.3 %RANDOM
Rwork0.18792 ---
all0.1895 17376 --
obs0.1895 17376 98.9 %-
Displacement parametersBiso mean: 32.317 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2403 0 29 134 2566
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.021
X-RAY DIFFRACTIONp_mcbond_it2.1011.5
X-RAY DIFFRACTIONp_mcangle_it3.4362
X-RAY DIFFRACTIONp_scbond_it4.9363
X-RAY DIFFRACTIONp_scangle_it7.54.5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 4.3 % / Rfactor obs: 0.188
Solvent computation
*PLUS
Displacement parameters
*PLUS

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