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- PDB-5ud3: Class II fructose-1,6-bisphosphate aldolase H180Q variant of Heli... -

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Basic information

Entry
Database: PDB / ID: 5ud3
TitleClass II fructose-1,6-bisphosphate aldolase H180Q variant of Helicobacter pylori with FBP
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / Glycolysis / Metalloenzyme
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 1. / 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
1,6-di-O-phosphono-D-fructose / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.44 Å
AuthorsJacques, B. / Sygusch, J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Active site remodeling during the catalytic cycle in metal-dependent fructose-1,6-bisphosphate aldolases.
Authors: Jacques, B. / Coincon, M. / Sygusch, J.
History
DepositionDec 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2018Provider: repository / Type: Initial release
Revision 1.1May 30, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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-bisphosphate aldolase
B: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,56910
Polymers67,5822
Non-polymers9888
Water13,097727
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-176 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.480, 64.904, 62.706
Angle α, β, γ (deg.)82.10, 74.17, 75.83
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Fructose-bisphosphate aldolase / / FBPA / Fructose-1 / 6-bisphosphate aldolase


Mass: 33790.797 Da / Num. of mol.: 2 / Mutation: H180Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: fba, HP_0176 / Production host: Escherichia coli (E. coli) / References: UniProt: P56109, fructose-bisphosphate aldolase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-P6F / 1,6-di-O-phosphono-D-fructose


Mass: 340.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O12P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 727 / 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: 2.21 Å3/Da / Density % sol: 44.38 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, PEG 1000, Calcium acetate, Tris-Acetic acid buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.44→37.073 Å / Num. obs: 97445 / % possible obs: 88.71 % / Redundancy: 1.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.05205 / Net I/σ(I): 8.93

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C4U

3c4u


Resolution: 1.44→37.073 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 17.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1643 3820 4.11 %
Rwork0.1345 --
obs0.1357 93003 88.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.44→37.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4534 0 46 727 5307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064813
X-RAY DIFFRACTIONf_angle_d0.8686499
X-RAY DIFFRACTIONf_dihedral_angle_d20.0981815
X-RAY DIFFRACTIONf_chiral_restr0.067715
X-RAY DIFFRACTIONf_plane_restr0.004852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.44-1.45820.2188840.20192326X-RAY DIFFRACTION62
1.4582-1.47740.24691360.1892452X-RAY DIFFRACTION68
1.4774-1.49770.19211050.17752743X-RAY DIFFRACTION73
1.4977-1.51910.2261270.16972858X-RAY DIFFRACTION77
1.5191-1.54170.19761140.16552992X-RAY DIFFRACTION81
1.5417-1.56580.20451360.15623170X-RAY DIFFRACTION83
1.5658-1.59150.21141330.15163138X-RAY DIFFRACTION85
1.5915-1.61890.21081420.143199X-RAY DIFFRACTION86
1.6189-1.64840.17991390.13593262X-RAY DIFFRACTION86
1.6484-1.68010.16421500.13533257X-RAY DIFFRACTION89
1.6801-1.71440.15341170.13713346X-RAY DIFFRACTION89
1.7144-1.75160.18641570.13373364X-RAY DIFFRACTION91
1.7516-1.79240.17171550.13073352X-RAY DIFFRACTION90
1.7924-1.83720.18151280.12763404X-RAY DIFFRACTION91
1.8372-1.88690.15821490.13193436X-RAY DIFFRACTION92
1.8869-1.94240.16111650.12913454X-RAY DIFFRACTION93
1.9424-2.00510.16791510.1333490X-RAY DIFFRACTION93
2.0051-2.07680.17261440.12813513X-RAY DIFFRACTION94
2.0768-2.15990.16071630.13063561X-RAY DIFFRACTION96
2.1599-2.25820.1471570.12133521X-RAY DIFFRACTION95
2.2582-2.37720.14821420.12213562X-RAY DIFFRACTION96
2.3772-2.52610.15861590.13273616X-RAY DIFFRACTION97
2.5261-2.72110.19171580.13853588X-RAY DIFFRACTION97
2.7211-2.99490.15671490.14083641X-RAY DIFFRACTION97
2.9949-3.4280.1671630.14293607X-RAY DIFFRACTION97
3.428-4.31780.15831520.11933650X-RAY DIFFRACTION98
4.3178-37.08570.12981450.13363681X-RAY DIFFRACTION99

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