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- PDB-6k96: Crystal structure of Ari2 -

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Basic information

Entry
Database: PDB / ID: 6k96
TitleCrystal structure of Ari2
ComponentsFive-membered-cyclitol-phosphate synthase
KeywordsOXIDOREDUCTASE / NAD binding / Rossmann fold
Function / homology
Function and homology information


inositol-3-phosphate synthase activity / inositol biosynthetic process / phospholipid biosynthetic process / nucleotide binding
Similarity search - Function
: / Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase / Myo-inositol-1-phosphate synthase, GAPDH-like / Myo-inositol-1-phosphate synthase / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Five-membered-cyclitol-phosphate synthase
Similarity search - Component
Biological speciesStreptomyces citricolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMiyanaga, A. / Tsunoda, T. / Kudo, F. / Eguchi, T.
CitationJournal: Biochemistry / Year: 2019
Title: Stereochemistry in the Reaction of themyo-Inositol Phosphate Synthase Ortholog Ari2 during Aristeromycin Biosynthesis.
Authors: Kudo, F. / Tsunoda, T. / Yamaguchi, K. / Miyanaga, A. / Eguchi, T.
History
DepositionJun 14, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 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_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_asym_id / _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: Five-membered-cyclitol-phosphate synthase
B: Five-membered-cyclitol-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0669
Polymers80,4172
Non-polymers1,6497
Water3,765209
1
A: Five-membered-cyclitol-phosphate synthase
B: Five-membered-cyclitol-phosphate synthase
hetero molecules

A: Five-membered-cyclitol-phosphate synthase
B: Five-membered-cyclitol-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,13218
Polymers160,8344
Non-polymers3,29814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/61
Buried area17380 Å2
ΔGint-145 kcal/mol
Surface area49620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.180, 101.180, 389.662
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 3 - 354 / Label seq-ID: 3 - 354

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Five-membered-cyclitol-phosphate synthase


Mass: 40208.402 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces citricolor (bacteria) / Gene: ari2 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1B4ZC85
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 3.58 Å3/Da / Density % sol: 65.64 %
Crystal growTemperature: 278 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tris-HCl, sodium chloride, sodium citrate, NAD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 9, 2014
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 40934 / % possible obs: 97.4 % / Redundancy: 8.4 % / Biso Wilson estimate: 38.7 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.138 / Net I/σ(I): 12.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 4.6 / Num. unique obs: 5751 / CC1/2: 0.867 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GR0

1gr0


Resolution: 2.5→47.18 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.872 / SU B: 23.556 / SU ML: 0.229 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2804 2061 5 %RANDOM
Rwork0.2263 ---
obs0.229 38772 96.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.32 Å2 / Biso mean: 42.74 Å2 / Biso min: 18.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-0.36 Å20 Å2
2---0.72 Å20 Å2
3---2.33 Å2
Refinement stepCycle: final / Resolution: 2.5→47.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5048 0 108 209 5365
Biso mean--35.36 36.88 -
Num. residues----676
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135258
X-RAY DIFFRACTIONr_bond_other_d0.0090.0174978
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.6347141
X-RAY DIFFRACTIONr_angle_other_deg1.4211.57311505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7435671
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62321.807249
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.31615820
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8431537
X-RAY DIFFRACTIONr_chiral_restr0.0830.2687
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025921
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021064
Refine LS restraints NCS

Ens-ID: 1 / Number: 9618 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 139 -
Rwork0.302 2762 -
all-2901 -
obs--95.84 %
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)
10.51340.2570.16520.43060.36050.55680.04190.0282-0.02820.0055-0.0706-0.0156-0.0159-0.21340.02870.250.049-0.06940.4377-0.13420.056627.354-35.8216.977
20.6890.2116-0.08470.5464-0.22960.57710.09660.01840.0452-0.0947-0.0341-0.05650.02170.132-0.06250.24610.05480.00950.3593-0.14820.083976.115-25.39616.17
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 355
2X-RAY DIFFRACTION1A400 - 403
3X-RAY DIFFRACTION1A501 - 616
4X-RAY DIFFRACTION2B3 - 354
5X-RAY DIFFRACTION2B400 - 402
6X-RAY DIFFRACTION2B501 - 593

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