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- PDB-2ohd: Crystal structure of hypothetical molybdenum cofactor biosynthesi... -

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Basic information

Entry
Database: PDB / ID: 2ohd
TitleCrystal structure of hypothetical molybdenum cofactor biosynthesis protein C from Sulfolobus tokodaii
ComponentsProbable molybdenum cofactor biosynthesis protein C
KeywordsBIOSYNTHETIC PROTEIN / alpha + beta
Function / homology
Function and homology information


GTP 3',8'-cyclase activity / cyclic pyranopterin monophosphate synthase / cyclic pyranopterin monophosphate synthase activity / Mo-molybdopterin cofactor biosynthetic process
Similarity search - Function
Probable cyclic pyranopterin monophosphate synthase accessory protein, archaea / Molybdopterin cofactor biosynthesis C (MoaC) domain / Molybdopterin cofactor biosynthesis C (MoaC) domain / Molybdenum cofactor biosynthesis C / Molybdopterin cofactor biosynthesis C (MoaC) domain superfamily / MoaC family / : / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable cyclic pyranopterin monophosphate synthase
Similarity search - Component
Biological speciesSulfolobus tokodaii str. 7 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYoshida, H. / Yamada, M. / Kuramitsu, S. / Kamitori, S.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Structure of a putative molybdenum-cofactor biosynthesis protein C (MoaC) from Sulfolobus tokodaii (ST0472)
Authors: Yoshida, H. / Yamada, M. / Kuramitsu, S. / Kamitori, S.
History
DepositionJan 10, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / 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

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Assembly

Deposited unit
A: Probable molybdenum cofactor biosynthesis protein C
B: Probable molybdenum cofactor biosynthesis protein C
C: Probable molybdenum cofactor biosynthesis protein C
D: Probable molybdenum cofactor biosynthesis protein C
E: Probable molybdenum cofactor biosynthesis protein C
F: Probable molybdenum cofactor biosynthesis protein C


Theoretical massNumber of molelcules
Total (without water)102,9136
Polymers102,9136
Non-polymers00
Water7,981443
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19850 Å2
ΔGint-121 kcal/mol
Surface area28360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)123.310, 78.578, 112.671
Angle α, β, γ (deg.)90.00, 118.06, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Probable molybdenum cofactor biosynthesis protein C


Mass: 17152.123 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii str. 7 (archaea) / Species: Sulfolobus tokodaii / Strain: strain 7 / Gene: ST0472 / Production host: Escherichia coli (E. coli) / References: UniProt: Q975D5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 443 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 18% PEG 3000, 0.1M HEPES, 0.2M magnesium chloride , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2006
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 48362 / Num. obs: 48362 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 15.2 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 11.3
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.268 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EKR

1ekr


Resolution: 2.2→45.78 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 52270.57 / 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
Rfree0.252 4645 10.1 %RANDOM
Rwork0.202 ---
all0.206 46051 --
obs0.202 46051 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.5666 Å2 / ksol: 0.373335 e/Å3
Displacement parametersBiso mean: 29.4 Å2
Baniso -1Baniso -2Baniso -3
1--3.84 Å20 Å2-2.3 Å2
2--13.51 Å20 Å2
3----9.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.2→45.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6687 0 0 443 7130
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.82
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 705 10.1 %
Rwork0.276 6304 -
obs--87.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramwater.top
X-RAY DIFFRACTION3ion.paramcarbohydrate.top
X-RAY DIFFRACTION4water_rep.paramion.top

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