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- PDB-4to8: Methicillin-Resistant Staphylococcus Aureus Class IIb Fructose 1,... -

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Basic information

Entry
Database: PDB / ID: 4to8
TitleMethicillin-Resistant Staphylococcus Aureus Class IIb Fructose 1,6-Bisphosphate Aldolase
ComponentsFructose-1,6-bisphosphate aldolase, class II
KeywordsLYASE / ZINC ENZYME / Methicillin Resistant / ALDOL CONDENSATION / GLYCOLYSIS / METAL-BINDING
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / fructose 1,6-bisphosphate metabolic process / glycolytic process / zinc ion binding
Similarity search - Function
Fructose-1,6-bisphosphate aldolase, class 2 / Fructose-bisphosphate aldolase class-II signature 2. / Fructose-bisphosphate aldolase, class-II / Fructose-bisphosphate aldolase class-II / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
CITRATE ANION / Fructose-1,6-bisphosphate aldolase
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.1 Å
AuthorsCapodagli, G.C. / Pegan, S.D.
CitationJournal: Biochemistry / Year: 2014
Title: Structural and Functional Characterization of Methicillin-Resistant Staphylococcus aureus's Class IIb Fructose 1,6-Bisphosphate Aldolase.
Authors: Capodagli, G.C. / Lee, S.A. / Boehm, K.J. / Brady, K.M. / Pegan, S.D.
History
DepositionJun 5, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Dec 27, 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 / refine_hist / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-1,6-bisphosphate aldolase, class II
B: Fructose-1,6-bisphosphate aldolase, class II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9116
Polymers63,4022
Non-polymers5094
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-92 kcal/mol
Surface area21710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.464, 96.054, 101.231
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 Fructose-1,6-bisphosphate aldolase, class II / Fructose-bisphosphate aldolase


Mass: 31700.893 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: fba, CH52_08335, X998_2104 / Plasmid: PET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W8TRN9, fructose-bisphosphate aldolase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C6H5O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 342 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.34 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop / Details: ammonium citrate / PH range: 6.0-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Nov 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→61.174 Å / Num. obs: 44357 / % possible obs: 99.3 % / Redundancy: 7.1 % / Net I/σ(I): 12.1
Reflection shellResolution: 2.1→2.173 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.761 / Mean I/σ(I) obs: 2.31 / % possible all: 97.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.4_1496) / Classification: refinement
RefinementResolution: 2.1→51.502 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2282 1989 4.51 %
Rwork0.1764 --
obs0.1787 44070 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→51.502 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4210 0 28 342 4580
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094355
X-RAY DIFFRACTIONf_angle_d15873
X-RAY DIFFRACTIONf_dihedral_angle_d13.8641645
X-RAY DIFFRACTIONf_chiral_restr0.038671
X-RAY DIFFRACTIONf_plane_restr0.005767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.15230.31051310.22272869X-RAY DIFFRACTION95
2.1523-2.21050.24071370.20622935X-RAY DIFFRACTION100
2.2105-2.27550.27431550.20862975X-RAY DIFFRACTION100
2.2755-2.3490.24171290.192976X-RAY DIFFRACTION100
2.349-2.43290.22641530.19072956X-RAY DIFFRACTION100
2.4329-2.53030.2421340.19133018X-RAY DIFFRACTION100
2.5303-2.64550.24381370.19952981X-RAY DIFFRACTION100
2.6455-2.7850.28771390.1922994X-RAY DIFFRACTION100
2.785-2.95940.25541500.20433005X-RAY DIFFRACTION100
2.9594-3.18790.25221410.19863015X-RAY DIFFRACTION100
3.1879-3.50860.25191390.16923024X-RAY DIFFRACTION100
3.5086-4.01620.17351480.14513041X-RAY DIFFRACTION100
4.0162-5.05930.17291470.13133080X-RAY DIFFRACTION100
5.0593-51.51790.19881490.15383212X-RAY DIFFRACTION100

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