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- PDB-3q1y: Allosteric regulation by Lysine residue: A novel anion-hole forma... -

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Basic information

Entry
Database: PDB / ID: 3q1y
TitleAllosteric regulation by Lysine residue: A novel anion-hole formation in the ribokinase family
ComponentsLin2199 protein
KeywordsTRANSFERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / PSI-II / ATP-BINDING
Function / homology
Function and homology information


lactose metabolic process / tagatose-6-phosphate kinase / phosphofructokinase activity / D-tagatose 6-phosphate catabolic process / tagatose-6-phosphate kinase activity / ATP binding / metal ion binding / cytosol
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
: / Tagatose-6-phosphate kinase
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsSatyanarayana, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Allosteric regulation by Lysine residue: A novel anion-hole formation in the ribokinase family
Authors: Satyanarayan, L. / Burley, S.K. / Swaminathan, S.
History
DepositionDec 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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 1.3Sep 13, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lin2199 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0833
Polymers34,9521
Non-polymers1312
Water2,054114
1
A: Lin2199 protein
hetero molecules

A: Lin2199 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1666
Polymers69,9042
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3220 Å2
ΔGint-2 kcal/mol
Surface area25700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.912, 44.717, 87.955
Angle α, β, γ (deg.)90.00, 113.48, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Lin2199 protein


Mass: 34951.941 Da / Num. of mol.: 1 / Mutation: K281A
Source method: isolated from a genetically manipulated source
Details: Top10 cells (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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M MgCl2,200mMCsCl, 20% PEG 3350 0.1M Bis-Tris pH 6.5), VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2010 / 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: 2.05→50 Å / Num. all: 20195 / Num. obs: 20195 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Rsym value: 0.087 / Net I/σ(I): 6.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 10.1 / Num. unique all: 1901 / Rsym value: 0.294 / % possible all: 94

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
DENZOdata reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HIC

3hic


Resolution: 2.03→50 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.799 / SU ML: 0.108 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.203 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 998 5 %RANDOM
Rwork0.1879 ---
obs0.1899 20154 97.51 %-
all-19156 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 47.52 Å2 / Biso mean: 23.675 Å2 / Biso min: 2.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.05 Å2
2--0.56 Å20 Å2
3----0.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.039 Å0.203 Å
Luzzati d res low-5 Å
Luzzati sigma a0.5 Å0.171 Å
Refinement stepCycle: LAST / Resolution: 2.03→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2357 0 7 114 2478
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222393
X-RAY DIFFRACTIONr_angle_refined_deg1.0881.9833227
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7845308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03925.97997
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33215443
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.802158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211738
X-RAY DIFFRACTIONr_mcbond_it0.5561.51533
X-RAY DIFFRACTIONr_mcangle_it1.07422470
X-RAY DIFFRACTIONr_scbond_it1.7123860
X-RAY DIFFRACTIONr_scangle_it2.9534.5757
LS refinement shellResolution: 2.033→2.085 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 51 -
Rwork0.2 1002 -
all-1053 -
obs--70.58 %

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