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- PDB-2pbq: Crystal structure of molybdenum cofactor biosynthesis (aq_061) Fr... -

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Basic information

Entry
Database: PDB / ID: 2pbq
TitleCrystal structure of molybdenum cofactor biosynthesis (aq_061) From aquifex aeolicus VF5
ComponentsMolybdenum cofactor biosynthesis MOG
KeywordsLYASE / molybdopterin / MPT / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Mo-molybdopterin cofactor biosynthetic process
Similarity search - Function
Molybdenum cofactor biosynthesis proteins signature 1. / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Molybdenum cofactor biosynthesis MOG
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsJeyakanthan, J. / Mahesh, S. / Kanaujia, S.P. / Ramakumar, S. / Sekar, K. / Agari, Y. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. ...Jeyakanthan, J. / Mahesh, S. / Kanaujia, S.P. / Ramakumar, S. / 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 molybdenum cofactor biosynthesis (aq_061) from aquifex aeolicus VF5
Authors: Jeyakanthan, J. / Mahesh, S. / Kanaujia, S.P. / Ramakumar, S. / Sekar, K. / Agari, Y. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S.
History
DepositionMar 29, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Molybdenum cofactor biosynthesis MOG
B: Molybdenum cofactor biosynthesis MOG
C: Molybdenum cofactor biosynthesis MOG


Theoretical massNumber of molelcules
Total (without water)57,8963
Polymers57,8963
Non-polymers00
Water11,187621
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-32 kcal/mol
Surface area20830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)39.409, 113.159, 55.980
Angle α, β, γ (deg.)90.00, 93.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Molybdenum cofactor biosynthesis MOG


Mass: 19298.580 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: PET21A / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 CONDON PLUS (DE3)-RIL / References: UniProt: O66472
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 621 / 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: 2.15 Å3/Da / Density % sol: 42.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 40% PEG 600, 100mM CES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 18, 2006 / Details: RH Coated Bent-Cyrindrical MIRROR
RadiationMonochromator: SI 1 1 1 Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 53022 / % possible obs: 99.6 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.054
Reflection shellResolution: 1.7→1.76 Å / Rmerge(I) obs: 0.23 / Num. unique all: 5250 / Rsym value: 0.267 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FUW

2fuw
PDB Unreleased entry


Resolution: 1.7→39.76 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2176617.77 / 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
Rfree0.225 5266 10.1 %RANDOM
Rwork0.195 ---
obs0.195 51884 96.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.8727 Å2 / ksol: 0.341023 e/Å3
Displacement parametersBiso mean: 26.4 Å2
Baniso -1Baniso -2Baniso -3
1-4.3 Å20 Å2-1.61 Å2
2--2.11 Å20 Å2
3----6.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 1.7→39.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3858 0 0 621 4479
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.29 607 10.5 %
Rwork0.256 5155 -
obs--86.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION5water_rep.paramwater_protin.top

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