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- PDB-2omd: Crystal structure of molybdopterin converting factor subunit 2 (a... -

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Basic information

Entry
Database: PDB / ID: 2omd
TitleCrystal structure of molybdopterin converting factor subunit 2 (aq_2181) from aquifex aeolicus VF5
ComponentsMolybdopterin-converting factor subunit 2
KeywordsLYASE / MOAE / coenzyme biosynthesis / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


molybdopterin synthase activity / molybdopterin synthase / Mo-molybdopterin cofactor biosynthetic process / cytosol
Similarity search - Function
Molybdopterin biosynthesis MoaE subunit / Molybdopterin biosynthesis MoaE / Molybdopterin biosynthesis MoaE subunit superfamily / MoaE protein / Aldehyde Oxidoreductase; domain 3 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Molybdopterin synthase catalytic subunit
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsJeyakanthan, J. / Kanaujia, S.P. / Vasuki Ranjani, C. / Sekar, K. / Agari, Y. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of molybdopterin converting factor subunit 2 (aq_2181) from aquifex aeolicus VF5
Authors: Jeyakanthan, J. / Kanaujia, S.P. / Vasuki Ranjani, C. / Sekar, K. / Agari, Y. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S.
History
DepositionJan 22, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Dec 27, 2023Group: 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-converting factor subunit 2
B: Molybdopterin-converting factor subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,69210
Polymers35,2132
Non-polymers4808
Water6,828379
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.995, 119.995, 125.804
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Molybdopterin-converting factor subunit 2 / MPT synthase subunit 2 / Molybdopterin synthase subunit 2 / Molybdenum cofactor biosynthesis ...MPT synthase subunit 2 / Molybdopterin synthase subunit 2 / Molybdenum cofactor biosynthesis protein E / Molybdopterin-converting factor large subunit


Mass: 17606.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: PET21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21(DE3)-RIL / References: UniProt: O67928

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Non-polymers , 6 types, 387 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 379 / 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: 3.71 Å3/Da / Density % sol: 66.86 %
Crystal growTemperature: 291 K / Method: microbatch
Details: 10% 1,2-propanediol, 25% Glycerol, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9788, 0.9000, 0.9794
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 15, 2006 / Details: RH Coated Bent-Cyrindrical MIRROR
RadiationMonochromator: SI 1 1 1 Double Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.91
30.97941
ReflectionResolution: 2→50 Å / Num. obs: 36659 / % possible obs: 100 % / Biso Wilson estimate: 25.6 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.073
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.249 / Num. unique all: 3583 / Rsym value: 0.264 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→38.89 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1319976.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3590 10 %RANDOM
Rwork0.19 ---
obs0.19 35966 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.8037 Å2 / ksol: 0.339765 e/Å3
Displacement parametersBiso mean: 32 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20.99 Å20 Å2
2--0.24 Å20 Å2
3----0.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→38.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 29 379 2675
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.245 405 9.5 %
Rwork0.207 3879 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ligand.paramligand.top
X-RAY DIFFRACTION5water_rep.paramwater_protin.top

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