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- PDB-6af2: Crystal structure of N-terminus deletion mutant of Mycobacterium ... -

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Basic information

Entry
Database: PDB / ID: 6af2
TitleCrystal structure of N-terminus deletion mutant of Mycobacterium avium diadenosine 5',5'''-P1,P4-tetraphosphate phosphorylase
ComponentsHIT domain-containing protein
KeywordsTRANSFERASE / Nucleoside
Function / homology
Function and homology information


catalytic activity / nucleotide binding
Similarity search - Function
FHIT family / Histidine triad (HIT) protein / HIT domain / HIT domain profile. / HIT-like domain / HIT-like / HIT family, subunit A / HIT-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / SPERMINE / HIT domain-containing protein / HIT domain-containing protein
Similarity search - Component
Biological speciesMycobacterium avium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.001 Å
AuthorsMori, S. / Honda, N. / Kim, H. / Rimbara, E. / Shibayama, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K07377 Japan
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: To Be Published
Title: Crystal structure of N-terminus deletion mutant of Mycobacterium avium diadenosine tetraphosphate phosphorylase
Authors: Mori, S. / Honda, N. / Kim, H. / Rimbara, E. / Shibayama, K.
History
DepositionAug 8, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HIT domain-containing protein
B: HIT domain-containing protein
C: HIT domain-containing protein
D: HIT domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,88611
Polymers86,5914
Non-polymers1,2967
Water2,252125
1
A: HIT domain-containing protein
C: HIT domain-containing protein
hetero molecules

B: HIT domain-containing protein
D: HIT domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,88611
Polymers86,5914
Non-polymers1,2967
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area10980 Å2
ΔGint-57 kcal/mol
Surface area25100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.025, 104.837, 111.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))
21(chain B and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))
31(chain C and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))
41(chain D and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUGLNGLN(chain A and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))AA4 - 520 - 21
12THRTHRTHRTHR(chain A and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))AA1329
13ILEILEILEILE(chain A and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))AA42 - 15058 - 166
14GLNGLNSERSER(chain A and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))AA159 - 176175 - 192
21GLUGLUGLNGLN(chain B and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))BB36 - 3752 - 53
22THRTHRTHRTHR(chain B and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))BB4056
23ILEILEILEILE(chain B and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))BB42 - 15058 - 166
24GLNGLNSERSER(chain B and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))BB159 - 176175 - 192
31GLUGLUGLNGLN(chain C and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))CC36 - 3752 - 53
32THRTHRTHRTHR(chain C and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))CC4056
33ILEILEILEILE(chain C and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))CC42 - 15058 - 166
34GLNGLNSERSER(chain C and (resid 36 through 37 or resid 40 or resid 42 through 150 or resid 159 through 176))CC159 - 176175 - 192
41GLUGLUGLNGLN(chain D and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))DD4 - 520 - 21
42THRTHRTHRTHR(chain D and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))DD1329
43ILEILEILEILE(chain D and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))DD42 - 15058 - 166
44GLNGLNSERSER(chain D and (resid 4 through 5 or resid 13 or resid 42 through 150 or resid 159 through 176))DD159 - 176175 - 192

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Components

#1: Protein
HIT domain-containing protein / diadenosine 5' / 5'''-P1 / P4-tetraphosphate phosphorylase


Mass: 21647.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium avium (bacteria) / Gene: CKJ66_17020, CKJ75_15745 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2A2ZGT3, UniProt: Q73WE5*PLUS
#2: Chemical ChemComp-SPM / SPERMINE / Spermine


Mass: 202.340 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H26N4
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM Hepes (pH 7.6), 0.2 M CaCl2, 28% PEG 400, 2mM spermine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 16834 / % possible obs: 89.4 % / Redundancy: 9.5 % / Biso Wilson estimate: 44.97 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 12.1
Reflection shellResolution: 3→3.05 Å / Redundancy: 3 % / Rmerge(I) obs: 0.253 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 485 / % possible all: 54

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ANO
Resolution: 3.001→24.845 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 24.47
RfactorNum. reflection% reflection
Rfree0.266 861 5.13 %
Rwork0.2076 --
obs0.2107 16776 89.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 100.98 Å2 / Biso mean: 38.554 Å2 / Biso min: 12.41 Å2
Refinement stepCycle: final / Resolution: 3.001→24.845 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4453 0 88 125 4666
Biso mean--38.67 33.63 -
Num. residues----566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114630
X-RAY DIFFRACTIONf_angle_d1.5496258
X-RAY DIFFRACTIONf_chiral_restr0.083702
X-RAY DIFFRACTIONf_plane_restr0.011799
X-RAY DIFFRACTIONf_dihedral_angle_d9.1452759
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2374X-RAY DIFFRACTION16.558TORSIONAL
12B2374X-RAY DIFFRACTION16.558TORSIONAL
13C2374X-RAY DIFFRACTION16.558TORSIONAL
14D2374X-RAY DIFFRACTION16.558TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0012-3.18890.3499830.21591745182860
3.1889-3.43450.28411160.21252447256383
3.4345-3.77910.30751500.19562846299697
3.7791-4.32340.23951680.18062881304998
4.3234-5.43770.24021490.18992950309998
5.4377-24.84590.25861950.24273046324199

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