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- PDB-4lhb: Crystal structure of tungsten cofactor synthesizing protein MoaB ... -

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Basic information

Entry
Database: PDB / ID: 4lhb
TitleCrystal structure of tungsten cofactor synthesizing protein MoaB from Pyrococcus furiosus
ComponentsMolybdopterin adenylyltransferase
KeywordsTRANSFERASE / adenylylation of molybdopterin
Function / homology
Function and homology information


molybdopterin adenylyltransferase / molybdopterin adenylyltransferase activity / Mo-molybdopterin cofactor biosynthetic process / ATP binding
Similarity search - Function
Molybdenum cofactor biosynthesis protein MoaB / 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 speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHavarushka, N. / Schwarz, G.
CitationJournal: Plos One / Year: 2014
Title: Structural Basis of Thermal Stability of the Tungsten Cofactor Synthesis Protein MoaB from Pyrococcus furiosus.
Authors: Havarushka, N. / Fischer-Schrader, K. / Lamkemeyer, T. / Schwarz, G.
History
DepositionJul 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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 adenylyltransferase
B: Molybdopterin adenylyltransferase
C: Molybdopterin adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9166
Polymers61,6283
Non-polymers2883
Water2,090116
1
A: Molybdopterin adenylyltransferase
B: Molybdopterin adenylyltransferase
C: Molybdopterin adenylyltransferase
hetero molecules

A: Molybdopterin adenylyltransferase
B: Molybdopterin adenylyltransferase
C: Molybdopterin adenylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,83212
Polymers123,2566
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-1/31
Buried area17750 Å2
ΔGint-144 kcal/mol
Surface area35430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.939, 125.939, 73.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Molybdopterin adenylyltransferase / / MPT adenylyltransferase


Mass: 20542.627 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Strain: DSM 3638 / JCM 8422 / Vc1 / Gene: moaB, PF0372 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8U3T3, molybdopterin adenylyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.73 Å3/Da / Density % sol: 54.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1 MES pH 6.0, 40 % PEG 400, 5% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2009
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2.5→41.22 Å / Num. all: 22319 / Num. obs: 22319 / % possible obs: 99.97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.565 Å / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Y5E

1y5e


Resolution: 2.5→41.22 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.23122 1211 RANDOM
Rwork0.17727 --
all0.18009 22319 -
obs0.18009 22319 -
Refinement stepCycle: LAST / Resolution: 2.5→41.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3691 0 15 116 3822
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.016
X-RAY DIFFRACTIONr_bond_other_d0.001
X-RAY DIFFRACTIONr_angle_refined_deg1.938
X-RAY DIFFRACTIONr_angle_other_deg1.07
X-RAY DIFFRACTIONr_chiral_restr0.124

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