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- PDB-6pe3: Structure of YcaO enzyme from Methanocaldococcus jannaschii in co... -

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Basic information

Entry
Database: PDB / ID: 6pe3
TitleStructure of YcaO enzyme from Methanocaldococcus jannaschii in complex with ATP
ComponentsUncharacterized protein MJ1094
KeywordsBIOSYNTHETIC PROTEIN / YcaO / ATP / thioamide / Methanocaldococcus jannaschii
Function / homologyPutative methanogenesis marker protein 1 / YcaO-like domain / YcaO cyclodehydratase, ATP-ad Mg2+-binding / YcaO domain profile. / ADENOSINE-5'-TRIPHOSPHATE / Uncharacterized protein MJ1094
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDong, S.-H. / Nair, S.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM079038 United States
CitationJournal: Acs Cent.Sci. / Year: 2019
Title: Mechanistic Basis for Ribosomal Peptide Backbone Modifications.
Authors: Dong, S.H. / Liu, A. / Mahanta, N. / Mitchell, D.A. / Nair, S.K.
History
DepositionJun 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein MJ1094
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7362
Polymers44,2291
Non-polymers5071
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-2 kcal/mol
Surface area16890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.841, 106.841, 182.556
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-660-

HOH

21A-757-

HOH

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Components

#1: Protein Uncharacterized protein MJ1094


Mass: 44228.992 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ1094 / Production host: Escherichia coli (E. coli) / References: UniProt: Q58494
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 172 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.53 Å3/Da / Density % sol: 65.17 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 4.6, 2.0 M ammonium sulfate, 0.02 M taurine

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: liquid nitrogen flow / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979106 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979106 Å / Relative weight: 1
ReflectionResolution: 2.3→25.6 Å / Num. obs: 26776 / % possible obs: 95.61 % / Redundancy: 30.1 % / Net I/σ(I): 19.9
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 1846

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACTdata extraction
autoPROCdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.935 / SU B: 8.194 / SU ML: 0.183 / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.212 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25054 1391 5.2 %RANDOM
Rwork0.20111 ---
obs0.20352 25367 95.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 68.259 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å20.84 Å20 Å2
2--1.69 Å20 Å2
3----5.47 Å2
Refinement stepCycle: 1 / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2996 0 31 172 3199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0193083
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.994167
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1835370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94124.681141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.23215585
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.41519
X-RAY DIFFRACTIONr_chiral_restr0.1050.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212265
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.8676.5621486
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.6619.8291854
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.9386.961597
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined9.78390.5244752
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.304→2.363 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 105 -
Rwork0.346 1846 -
obs--98.04 %

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