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- PDB-1i6n: 1.8 A Crystal structure of IOLI protein with a binding zinc atom -

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Basic information

Entry
Database: PDB / ID: 1i6n
Title1.8 A Crystal structure of IOLI protein with a binding zinc atom
ComponentsIOLI PROTEIN
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / BETA BARREL / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


2-keto-myo-inositol isomerase / isomerase activity / metal ion binding
Similarity search - Function
: / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, R.G. / Dementiva, I. / Collart, F. / Quaite-Randall, E. / Joachimiak, A. / Alkire, R. / Maltsev, N. / Korolev, O. / Dieckman, L. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Proteins / Year: 2002
Title: Crystal structure of Bacillus subtilis ioli shows endonuclase IV fold with altered Zn binding.
Authors: Zhang, R.G. / Dementieva, I. / Duke, N. / Collart, F. / Quaite-Randall, E. / Alkire, R. / Dieckman, L. / Maltsev, N. / Korolev, O. / Joachimiak, A.
History
DepositionMar 2, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 9, 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_ref_seq_dif / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: IOLI PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,0412
Polymers31,9751
Non-polymers651
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.015, 104.616, 48.462
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein IOLI PROTEIN


Mass: 31975.344 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: IOLI OR B65B / Plasmid: PET30XALIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P42419
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.93 Å3/Da / Density % sol: 58.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.1
Details: Ammonium sulfate, Tris buffer, sodium chloride, EDTA, pH 8.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 8.4
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1250 mMimidazole1drop
220 mMTris-HCl1droppH8.4
30.15 mM1dropNaCl
42.5 mM1dropCaCl2
51.50-1.75 Mammonium sulfate1reservoir
60.050 MTris1reservoirpH8.00
70.10 M1reservoirNaCl
81.0 mMEDTA1reservoir
93.0 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.0332 Å
DetectorType: SBC-2 / Detector: CCD / Date: Aug 12, 2000 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.8→500 Å / Num. all: 35838 / Num. obs: 35623 / % possible obs: 99.4 % / Observed criterion σ(F): 6 / Observed criterion σ(I): 6 / Redundancy: 6.2 % / Biso Wilson estimate: 9.6 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 22.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.223 / Mean I/σ(I) obs: 6.1 / Num. unique all: 3449 / % possible all: 97.7

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Processing

Software
NameClassification
d*TREKdata scaling
HKL-2000data reduction
CNSrefinement
d*TREKdata reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1I60

1i60


Resolution: 1.8→19.9 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 365191.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 10000
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1737 5 %RANDOM
Rwork0.201 ---
all-35606 --
obs-34966 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.09 Å2 / ksol: 0.411 e/Å3
Displacement parametersBiso mean: 12.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---3.07 Å20 Å2
3---3.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å-0.04 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 1 174 2404
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_mcangle_it1.672
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.243 290 5.2 %
Rwork0.198 5294 -
obs--96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 % / Rfactor obs: 0.201
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 12.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69
X-RAY DIFFRACTIONc_mcbond_it1.311.5
X-RAY DIFFRACTIONc_scbond_it2.372
X-RAY DIFFRACTIONc_mcangle_it1.672
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.243 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.198

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