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- PDB-3hic: THE CRYSTAL STRUCTURE OF PHOSPHOFRUCTOKINASE(Lin2199)FROM Listeri... -

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Basic information

Entry
Database: PDB / ID: 3hic
TitleTHE CRYSTAL STRUCTURE OF PHOSPHOFRUCTOKINASE(Lin2199)FROM Listeria innocua
ComponentsLin2199 protein
KeywordsTRANSFERASE / Carbohydrate kinase / 1-phosphofructokinase / Phosphotransferase / NYSGXRC / 11206N / PSI2 / 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
Tagatose-6-phosphate kinase
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å
AuthorsSatyanarayana, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: THE CRYSTAL STRUCTURE OF PHOSPHOFRUCTOKINASE(Lin2199)FROM Listeria innocua
Authors: Satyanarayana, L. / Burley, S.K. / Swaminathan, S.
History
DepositionMay 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 13, 2019Group: Derived calculations / Structure summary / Category: struct_conn / struct_keywords
Item: _struct_conn.pdbx_leaving_atom_flag / _struct_keywords.text
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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

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Assembly

Deposited unit
A: Lin2199 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3632
Polymers35,3381
Non-polymers241
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lin2199 protein
hetero molecules

A: Lin2199 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7254
Polymers70,6772
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2200 Å2
ΔGint-15 kcal/mol
Surface area26740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.196, 44.598, 88.242
Angle α, β, γ (deg.)90.00, 113.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Lin2199 protein


Mass: 35338.305 Da / Num. of mol.: 1 / Fragment: Full length
Source method: isolated from a genetically manipulated source
Details: TOP10(Invitrogen) / Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin2199 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Codon+(RIL) / References: UniProt: Q929S5
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.28 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1M Bis-Tris pH 6.5 [100mM]+ 50% PEG 3350 [25%] + Lithium Sulfate [200mM], VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 1, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. all: 21120 / Num. obs: 21120 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.1 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 9.9
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.5 / Num. unique all: 1928 / Rsym value: 0.459 / % possible all: 92.1

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXCDphasing
SHARPphasing
CNS1.1refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.02→40.91 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 796 -RANDOM
Rwork0.217 ---
all0.228 20217 --
obs0.217 20217 95.4 %-
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å20 Å20.95 Å2
2---1.35 Å20 Å2
3----0.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.02→40.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2335 0 1 233 2569
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_degree23.3
X-RAY DIFFRACTIONc_improper_angle_deg0.76
LS refinement shellResolution: 2.02→2.15 Å / Rfactor Rfree error: 0.035
RfactorNum. reflection% reflection
Rfree0.365 110 -
Rwork0.301 --
obs-3011 89.7 %

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