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- PDB-2qq1: Crystal Structure Of Molybdenum Cofactor Biosynthesis (aq_061) Ot... -

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Basic information

Entry
Database: PDB / ID: 2qq1
TitleCrystal Structure Of Molybdenum Cofactor Biosynthesis (aq_061) Other Form From Aquifex Aeolicus Vf5
ComponentsMolybdenum cofactor biosynthesis MOG
KeywordsSTRUCTURAL PROTEIN / 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


molybdopterin cofactor biosynthetic process / molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / Mo-molybdopterin cofactor biosynthetic process / cytosol
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
Molybdopterin adenylyltransferase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJeyakanthan, J. / Mahesh, S. / Kanaujia, S.P. / Ramakumar, S. / Sekar, K. / Agari, Y. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure Of Molybdenum Cofactor Biosynthesis (aq_061) Other Form From Aquifex Aeolicus Vf5
Authors: Jeyakanthan, J. / Mahesh, S. / Kanaujia, S.P. / Ramakumar, S. / Sekar, K. / Agari, Y. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Yokoyama, S.
History
DepositionJul 26, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 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

Downloads & links

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Assembly

Deposited unit
A: Molybdenum cofactor biosynthesis MOG
B: Molybdenum cofactor biosynthesis MOG
C: Molybdenum cofactor biosynthesis MOG
D: Molybdenum cofactor biosynthesis MOG
E: Molybdenum cofactor biosynthesis MOG
F: Molybdenum cofactor biosynthesis MOG


Theoretical massNumber of molelcules
Total (without water)115,7916
Polymers115,7916
Non-polymers00
Water18,4111022
1
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
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-34.6 kcal/mol
Surface area21620 Å2
MethodPISA
2
D: Molybdenum cofactor biosynthesis MOG
E: Molybdenum cofactor biosynthesis MOG
F: Molybdenum cofactor biosynthesis MOG


Theoretical massNumber of molelcules
Total (without water)57,8963
Polymers57,8963
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-33.2 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.015, 64.074, 102.342
Angle α, β, γ (deg.)95.11, 98.05, 106.89
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Molybdenum cofactor biosynthesis MOG


Mass: 19298.580 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: mog / 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


Mass: 18.015 Da / Num. of mol.: 1022 / 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: 2.13 Å3/Da / Density % sol: 42.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M ammonium acetate, 0.1M bis-tris, 25% PEG3350, pH5.5, 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 19, 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: 1.9→50 Å / Num. obs: 71606 / % possible obs: 96.4 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.043 / Rsym value: 0.044
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.199 / Num. unique all: 7110 / Rsym value: 0.219 / % possible all: 95.5

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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: PDB ENTRY 2PBQ

2pbq


Resolution: 1.9→41.59 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1896629.83 / 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
Rfree0.242 3554 5.1 %RANDOM
Rwork0.206 ---
obs0.206 69944 93.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 64.0222 Å2 / ksol: 0.338792 e/Å3
Displacement parametersBiso mean: 36.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å24.27 Å24.03 Å2
2--2.62 Å22.87 Å2
3----2.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.9→41.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7899 0 0 1022 8921
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d0.93
LS refinement shellResolution: 1.9→1.99 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.332 402 5.4 %
Rwork0.289 7036 -
obs--79.4 %
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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