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- PDB-3ot1: Crystal structure of VC2308 protein -

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Basic information

Entry
Database: PDB / ID: 3ot1
TitleCrystal structure of VC2308 protein
Components(4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme) x 2
KeywordsSTRUCTURAL GENOMICS / CSGID / Vibrio cholerae / Center for Structural Genomics of Infectious Diseases / DJ-1 superfamily / UNKNOWN FUNCTION
Function / homology
Function and homology information


Protein/nucleic acid deglycase DJ-1 / : / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.16 Å
AuthorsNiedzialkowska, E. / Wawrzak, Z. / Chruszcz, M. / Porebski, P. / Skarina, T. / Huang, X. / Grimshaw, S. / Cymborowski, M. / Savchenko, A. / Anderson, W.F. ...Niedzialkowska, E. / Wawrzak, Z. / Chruszcz, M. / Porebski, P. / Skarina, T. / Huang, X. / Grimshaw, S. / Cymborowski, M. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: Crystal structure of VC2308 protein
Authors: Niedzialkowska, E. / Wawrzak, Z. / Chruszcz, M. / Porebski, P. / Skarina, T. / Huang, X. / Grimshaw, S. / Cymborowski, M. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural ...Authors: Niedzialkowska, E. / Wawrzak, Z. / Chruszcz, M. / Porebski, P. / Skarina, T. / Huang, X. / Grimshaw, S. / Cymborowski, M. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 10, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme
B: 4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8215
Polymers44,7272
Non-polymers943
Water10,431579
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-49 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.387, 64.683, 81.592
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 4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme


Mass: 22355.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CYS at residue 108
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VC2308, VC_2308 / Plasmid: MCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 gold magic / References: UniProt: Q9KPQ8
#2: Protein 4-methyl-5(B-hydroxyethyl)-thiazole monophosphate biosynthesis enzyme


Mass: 22371.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CSX at residue 108
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: VC2308, VC_2308 / Plasmid: MCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 gold magic / References: UniProt: Q9KPQ8
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 579 / 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: 1.9 Å3/Da / Density % sol: 35.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Tacsimate 35%, Phenol 10mM, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 9, 2010 / Details: beryllium lenses
RadiationMonochromator: diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.16→50 Å / Num. all: 115862 / Num. obs: 115862 / % possible obs: 97.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.12 % / Rmerge(I) obs: 0.094 / Rsym value: 0.094 / Net I/σ(I): 23.8
Reflection shellResolution: 1.16→1.18 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 1.9 / Num. unique all: 4962 / Rsym value: 0.61 / % possible all: 84.5

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Processing

Software
NameVersionClassification
MD2data collection
HKL-3000MLPHAREphasing
DMmodel building
SHELXDphasing
SHELXEmodel building
ARP/wARPmodel building
CCP4model building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.16→50 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 0.981 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.037
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16775 5797 5 %RANDOM
Rwork0.14357 ---
all0.1448 109812 --
obs0.1448 109812 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.231 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 1.16→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2927 0 3 579 3509
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223236
X-RAY DIFFRACTIONr_bond_other_d0.0020.022120
X-RAY DIFFRACTIONr_angle_refined_deg1.51.9644447
X-RAY DIFFRACTIONr_angle_other_deg2.33435245
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0535460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.69724.427131
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.9815536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7881517
X-RAY DIFFRACTIONr_chiral_restr0.0910.2526
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213736
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02643
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_it1.2971.52100
X-RAY DIFFRACTIONr_mcbond_other1.5431.5850
X-RAY DIFFRACTIONr_mcangle_it1.93223390
X-RAY DIFFRACTIONr_scbond_it2.92631136
X-RAY DIFFRACTIONr_scangle_it4.2364.51032
X-RAY DIFFRACTIONr_rigid_bond_restr1.37333236
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.16→1.19 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 359 -
Rwork0.253 7215 -
obs--87.37 %

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