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- PDB-2gru: Crystal structure of 2-deoxy-scyllo-inosose synthase complexed wi... -

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Basic information

Entry
Database: PDB / ID: 2gru
TitleCrystal structure of 2-deoxy-scyllo-inosose synthase complexed with carbaglucose-6-phosphate, NAD+ and Co2+
Components2-deoxy-scyllo-inosose synthase
KeywordsLYASE / aminoglycoside / 2-deoxystreptamine / dehydroquinate synthase
Function / homology
Function and homology information


2-deoxy-scyllo-inosose synthase / 3-dehydroquinate synthase activity / aromatic amino acid family biosynthetic process / antibiotic biosynthetic process / metal ion binding
Similarity search - Function
3-dehydroquinate synthase family / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-CAK / : / Chem-EXO / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / PHOSPHATE ION / SULFITE ION / 2-deoxy-scyllo-inosose synthase
Similarity search - Component
Biological speciesBacillus circulans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsNango, E. / Kumasaka, T.
CitationJournal: Proteins / Year: 2008
Title: Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+
Authors: Nango, E. / Kumasaka, T. / Hirayama, T. / Tanaka, N. / Eguchi, T.
History
DepositionApr 25, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: 2-deoxy-scyllo-inosose synthase
B: 2-deoxy-scyllo-inosose synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,94013
Polymers81,5862
Non-polymers2,35411
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7450 Å2
ΔGint-68.9 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.569, 70.108, 81.569
Angle α, β, γ (deg.)90.00, 117.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 2-deoxy-scyllo-inosose synthase /


Mass: 40792.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus circulans (bacteria) / Plasmid: PET30B / Production host: Escherichia coli (E. coli)
References: UniProt: Q9S5E2, Lyases; Carbon-oxygen lyases; Acting on phosphates

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Non-polymers , 8 types, 331 molecules

#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-SO3 / SULFITE ION / Sulfite


Mass: 80.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#6: Chemical ChemComp-EXO / (1R,2S,3S,4R)-5-METHYLENECYCLOHEXANE-1,2,3,4-TETRAOL


Mass: 160.168 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H12O4
#7: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#8: Chemical ChemComp-CAK / [(1R,2R,3S,4S,5R)-2,3,4,5-TETRAHYDROXYCYCLOHEXYL]METHYL DIHYDROGEN PHOSPHATE / [(1R,2R,3S,4S,5R)-2,3,4,5-TETRAHYDROXYCYCLOHEXYL]METHYL PHOSPHORIC ACID


Mass: 258.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H15O8P
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: 40%(w/v) PEG 4000, 200mM Li2SO4, 100mM Tris-HCl, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Mar 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.15→72.36 Å / Num. all: 43452 / Num. obs: 43452 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.15→2.23 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SCALEPACKdata scaling
XFITdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB enrty 2D2X

2d2x


Resolution: 2.15→40.72 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.926 / SU B: 4.713 / SU ML: 0.125 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22257 2170 5 %RANDOM
Rwork0.17352 ---
all0.17599 40936 --
obs0.17599 40936 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.807 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.23 Å2
2--1.07 Å20 Å2
3----0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.15→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5717 0 130 336 6183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0225982
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9271.998117
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0625724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.60324.411263
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.251151020
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8181528
X-RAY DIFFRACTIONr_chiral_restr0.170.2925
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024429
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2370.22911
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.24064
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2358
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.253
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1681.53733
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.93725836
X-RAY DIFFRACTIONr_scbond_it3.0732551
X-RAY DIFFRACTIONr_scangle_it4.4744.52283
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 143 -
Rwork0.201 2908 -
obs--95.67 %

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