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- PDB-1uz5: The Crystal Structure of molybdopterin biosynthesis moea protein ... -

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Basic information

Entry
Database: PDB / ID: 1uz5
TitleThe Crystal Structure of molybdopterin biosynthesis moea protein from Pyrococcus horikosii
Components402AA LONG HYPOTHETICAL MOLYBDOPTERIN BIOSYNTHESIS MOEA PROTEIN
KeywordsMOLYBDOPTERIN BIOSYNTHESIS / MOEA MOLYBDOPTERIN / SYNTHESIS / MOCF BIOSYNTHESIS / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / STRUCTURAL GENOMICS
Function / homology
Function and homology information


molybdopterin cofactor biosynthetic process / Mo-molybdopterin cofactor biosynthetic process
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 / 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 ...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 / 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 / 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
402aa long hypothetical molybdopterin biosynthesis moea protein
Similarity search - Component
Biological speciesPYROCOCCUS HORIKOSHII (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsTakahashi, H. / Tahirov, T.H.
CitationJournal: To be Published
Title: The Crystal Structure of Molybdopterin Biosynthesis Moeaprotein from Pyrococcus Horikosii
Authors: Takahashi, H. / Miyano, M. / Tahirov, T.H.
History
DepositionMar 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2004Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AG" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 402AA LONG HYPOTHETICAL MOLYBDOPTERIN BIOSYNTHESIS MOEA PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4317
Polymers42,8551
Non-polymers5766
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)181.375, 181.375, 71.311
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein 402AA LONG HYPOTHETICAL MOLYBDOPTERIN BIOSYNTHESIS MOEA PROTEIN / MOEA PROTEIN


Mass: 42854.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS HORIKOSHII (archaea) / Strain: OT3 / Plasmid: PET 11A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O58335
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 4 Å3/Da / Density % sol: 68.1 %
Crystal growpH: 5.3
Details: CRYSTALLIZED FROM 1.1M LI SULFATE, 0.1M ACETATE, PH4., pH 5.30

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.97910, 0.97949, 1.000
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 15, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.979491
311
ReflectionResolution: 2.05→50 Å / Num. obs: 43761 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 11.4 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 23
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.096 / Mean I/σ(I) obs: 7.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→42.21 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1029241.6
RfactorNum. reflection% reflectionSelection details
Rfree0.247 4095 9.4 %RANDOM
Rwork0.218 ---
obs0.218 43532 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.44 Å24.56 Å20 Å2
2--2.44 Å20 Å2
3----4.88 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.05→42.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2919 0 30 242 3191
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.481.5
X-RAY DIFFRACTIONc_mcangle_it5.632
X-RAY DIFFRACTIONc_scbond_it6.622
X-RAY DIFFRACTIONc_scangle_it8.992.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 405 5.7 %
Rwork0.267 6705 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3CIS_PEPTIDE.PARAMSO4.TOP
X-RAY DIFFRACTION4SO4.PARAM

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