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- PDB-5yhh: Crystal structure of YiiM from Geobacillus stearothermophilus -

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Basic information

Entry
Database: PDB / ID: 5yhh
TitleCrystal structure of YiiM from Geobacillus stearothermophilus
ComponentsUncharacterized conserved protein YiiM
KeywordsOXIDOREDUCTASE / enzyme / MOSC
Function / homology
Function and homology information


molybdenum ion binding / catalytic activity / pyridoxal phosphate binding
Similarity search - Function
YiiM-like, 3-alpha helix domain / YiiM-like, 3-alpha helix domain / PK beta-barrel domain-like / MOSC domain / Molybdenum cofactor sulfurase, C-terminal / MOSC domain profile. / M1 Pyruvate Kinase; Domain 3 / Pyruvate kinase-like, insert domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
MOSC domain-containing protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNamgung, B. / Kim, J.H. / Song, W.S. / Yoon, S.I.
CitationJournal: Sci Rep / Year: 2018
Title: Crystal structure of the hydroxylaminopurine resistance protein, YiiM, and its putative molybdenum cofactor-binding catalytic site.
Authors: Namgung, B. / Kim, J.H. / Song, W.S. / Yoon, S.I.
History
DepositionSep 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 7, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: Uncharacterized conserved protein YiiM


Theoretical massNumber of molelcules
Total (without water)24,1941
Polymers24,1941
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.420, 51.526, 94.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Uncharacterized conserved protein YiiM / MOSC domain-containing protein


Mass: 24194.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: B4114_1419 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A150NEL9*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsThe sequence was based on database WP_033016727, and was not available at UNIPROT at the time of ...The sequence was based on database WP_033016727, and was not available at UNIPROT at the time of data annotation. N-terminal residues GSAKDP were from expression tag.

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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: 2.33 Å3/Da / Density % sol: 47.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.095M sodium citrate pH 5.6, 21% PEG 4000, 19% isopropanol, 5% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.00004 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 15858 / % possible obs: 99.7 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.066 / Net I/σ(I): 38.9
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 4.8

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O65

1o65


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.477 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.146 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22346 783 5 %RANDOM
Rwork0.18532 ---
obs0.18714 14960 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 38.907 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2---1.62 Å20 Å2
3---1.11 Å2
Refinement stepCycle: 1 / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1494 0 0 49 1543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221531
X-RAY DIFFRACTIONr_bond_other_d0.0030.021032
X-RAY DIFFRACTIONr_angle_refined_deg1.441.9552081
X-RAY DIFFRACTIONr_angle_other_deg0.90732520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0315192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05623.87162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78315242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.878157
X-RAY DIFFRACTIONr_chiral_restr0.0890.2230
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211694
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02302
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_it0.7981.5968
X-RAY DIFFRACTIONr_mcbond_other0.1971.5396
X-RAY DIFFRACTIONr_mcangle_it1.49121551
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2913563
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.5734.5530
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
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→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 47 -
Rwork0.256 1102 -
obs--99.05 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.2074-0.13250.10551.73220.37042.8142-0.21390.01880.04960.16880.0532-0.1058-0.0017-0.12440.16070.0960.0189-0.0250.3481-0.03380.0301-3.515-8.3479.504
26.2985-0.07320.71055.05681.61078.3452-0.27860.46640.8128-0.29520.2847-0.7831-0.71411.1074-0.00610.2266-0.1337-0.0710.49720.02430.329710.0816.2757.524
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 164
2X-RAY DIFFRACTION2A165 - 210

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