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- PDB-3jul: Crystal structure of Listeria innocua D-Tagatose-6-Phosphate Kina... -

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Basic information

Entry
Database: PDB / ID: 3jul
TitleCrystal structure of Listeria innocua D-Tagatose-6-Phosphate Kinase bound with substrate
ComponentsLin2199 protein
KeywordsTRANSFERASE / KINASE / ATP / LISTERIA INNOCUA / Tagatose-6-phosphate / MG+2 ION / 11206N1 / PSI-II / NYSGXRC / ATP-binding / Nucleotide-binding / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


lactose metabolic process / tagatose-6-phosphate kinase / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity / ATP binding / metal ion binding
Similarity search - Function
Tagatose/fructose phosphokinase / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
6-O-phosphono-beta-D-tagatofuranose / Tagatose-6-phosphate kinase
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsSatyanarayana, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Listeria innocua D-Tagatose-6-Phosphate Kinase bound with substrate
Authors: Satyanarayana, L. / Burley, S.K. / Swaminathan, S.
History
DepositionSep 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.occupancy / _chem_comp.name ..._atom_site.occupancy / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / chem_comp / citation_author
Item: _audit_author.identifier_ORCID / _chem_comp.pdbx_synonyms / _citation_author.identifier_ORCID
Revision 2.2Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lin2199 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6233
Polymers35,3381
Non-polymers2842
Water1,44180
1
A: Lin2199 protein
hetero molecules

A: Lin2199 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2456
Polymers70,6772
Non-polymers5694
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2410 Å2
ΔGint-13.4 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.307, 44.240, 79.116
Angle α, β, γ (deg.)90.00, 104.65, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-388-

HOH

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Components

#1: Protein Lin2199 protein


Mass: 35338.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Top10 (Invitrogen) / Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin2199 / Plasmid: pSGX3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Codon+RIL / References: UniProt: Q929S5, tagatose-6-phosphate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Sugar ChemComp-TA6 / 6-O-phosphono-beta-D-tagatofuranose / 6-O-phosphono-beta-D-tagatose / 6-O-phosphono-D-tagatose / 6-O-phosphono-tagatose


Type: D-saccharide, beta linking / Mass: 260.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13O9P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.02 Å3/Da / Density % sol: 39.1 %
Crystal growTemperature: 298 K / pH: 8.5
Details: 25% PEG 3350, 0.2M MgCl2, 0.1M Tris pH 8.5, 8mM Fructose-6-Phosphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 16, 2009 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 14658 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 6.4 % / Biso Wilson estimate: 21.3 Å2 / Rsym value: 0.097 / Net I/σ(I): 7.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.2 % / Mean I/σ(I) obs: 5.3 / Rsym value: 0.591 / % possible all: 94.3

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Processing

Software
NameVersionClassification
CBASSdata collection
MOLREPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3HIC

3hic


Resolution: 2.4→40.78 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.267 439 -RANDOM
Rwork0.226 ---
obs0.226 10640 94.5 %-
all-10640 --
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1--6.177 Å20 Å211.758 Å2
2--5.576 Å20 Å2
3---0.601 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.4→40.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2265 0 17 80 2362
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.3771.5
X-RAY DIFFRACTIONc_mcangle_it2.3252
X-RAY DIFFRACTIONc_scbond_it2.3242
X-RAY DIFFRACTIONc_scangle_it3.2422.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.048
RfactorNum. reflection% reflection
Rfree0.384 64 -
Rwork0.313 --
obs--86.3 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3ion.param
X-RAY DIFFRACTION4tagatose.par

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