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- PDB-6rs1: Dipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosph... -

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Basic information

Entry
Database: PDB / ID: 6rs1
TitleDipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosphate aldolase
ComponentsFructose-bisphosphate aldolase 6, cytosolic
KeywordsPEPTIDE BINDING PROTEIN / ----
Function / homology
Function and homology information


mitochondria-nucleus signaling pathway / salicylic acid binding / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / plasmodesma / gluconeogenesis / glycolytic process / cellular response to hypoxia / copper ion binding / mRNA binding ...mitochondria-nucleus signaling pathway / salicylic acid binding / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / plasmodesma / gluconeogenesis / glycolytic process / cellular response to hypoxia / copper ion binding / mRNA binding / endoplasmic reticulum / mitochondrion / nucleus / plasma membrane / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase class-I active site / Fructose-bisphosphate aldolase class-I active site. / Fructose-bisphosphate aldolase, class-I / Fructose-bisphosphate aldolase class-I / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Fructose-bisphosphate aldolase 6, cytosolic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsShahar, A. / Zarivach, R. / Skirycz, A. / Wojciechowska, I.
CitationJournal: To Be Published
Title: Dipeptide Gly-Pro binds to a glycolytic enzyme fructose bisphosphate aldolase
Authors: Wojciechowska, I. / Vogeli, B. / Shahar, A. / Szlachetko, J. / Gorka, M. / Sokolowska, E.M. / Veyel, D. / Silva, D.V. / Erb, T. / Zarivach, R. / Skirycz, A.
History
DepositionMay 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase 6, cytosolic
B: Fructose-bisphosphate aldolase 6, cytosolic
C: Fructose-bisphosphate aldolase 6, cytosolic
D: Fructose-bisphosphate aldolase 6, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,60013
Polymers153,7354
Non-polymers8659
Water11,061614
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-161 kcal/mol
Surface area50390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.567, 67.636, 88.908
Angle α, β, γ (deg.)79.95, 73.13, 65.58
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 4 - 340 / Label seq-ID: 4 - 340

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Fructose-bisphosphate aldolase 6, cytosolic / AtFBA6 / Cytosolic aldolase 2 / cAld2


Mass: 38433.766 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FBA6, At2g36460 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: Q9SJQ9, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 614 / 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: 2.3 Å3/Da / Density % sol: 46.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium Sulfate, 0.1 M Bis-Tris pH 6.2 and 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.072 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jun 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.9→48.37 Å / Num. obs: 88957 / % possible obs: 83.45 % / Redundancy: 4.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.09 / Rrim(I) all: 0.2 / Net I/σ(I): 7.04
Reflection shellResolution: 1.9→2.04 Å / Rmerge(I) obs: 1.194 / Num. unique obs: 4572 / CC1/2: 0.623 / Rpim(I) all: 0.6 / Rrim(I) all: 1.34

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KY6

5ky6


Resolution: 1.9→48.37 Å / Cor.coef. Fo:Fc: 0.903 / Cor.coef. Fo:Fc free: 0.867 / SU B: 11.687 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.212 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25381 3860 5 %RANDOM
Rwork0.21435 ---
obs0.21631 73398 71.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 20.153 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0.21 Å20.03 Å2
2--0.11 Å20.04 Å2
3----0.34 Å2
Refinement stepCycle: 1 / Resolution: 1.9→48.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10156 0 45 614 10815
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01410534
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179853
X-RAY DIFFRACTIONr_angle_refined_deg1.5661.6614298
X-RAY DIFFRACTIONr_angle_other_deg0.981.63623121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.60351396
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.9622.931481
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.854151859
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.2571559
X-RAY DIFFRACTIONr_chiral_restr0.080.21419
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211855
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021813
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7150.9965440
X-RAY DIFFRACTIONr_mcbond_other0.7140.9955439
X-RAY DIFFRACTIONr_mcangle_it1.2961.4866806
X-RAY DIFFRACTIONr_mcangle_other1.2961.4876807
X-RAY DIFFRACTIONr_scbond_it0.6221.0855094
X-RAY DIFFRACTIONr_scbond_other0.4881.0565056
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8831.557412
X-RAY DIFFRACTIONr_long_range_B_refined3.60412.34612010
X-RAY DIFFRACTIONr_long_range_B_other3.46212.2211874
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A110720.08
12B110720.08
21A110150.09
22C110150.09
31A111660.07
32D111660.07
41B110120.07
42C110120.07
51B109910.08
52D109910.08
61C109320.08
62D109320.08
LS refinement shellResolution: 1.9→1.945 Å
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork-0 -
obs--0 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0465-0.0349-0.36711.4942-0.29561.22-0.0039-0.19620.05360.2005-0.0122-0.0944-0.13440.12220.01610.0374-0.0038-0.02230.0428-0.01920.044715.77-2.031616.5542
21.31150.0340.2081.38720.07150.6568-0.0077-0.2904-0.09380.25590.02060.02530.0549-0.0392-0.01290.05180.0080.01290.06530.02510.048-15.854417.129119.7705
31.1824-0.08390.00951.27160.19410.76650.00670.20690.0075-0.31520.0013-0.0468-0.00480.0567-0.0080.0824-0.00010.020.0403-0.00190.0493-7.934422.3286-20.79
41.28690.0204-0.32731.1969-0.33720.9539-0.02330.1996-0.0241-0.22150.02960.13570.0527-0.15-0.00630.0423-0.0053-0.03060.0454-0.01480.0567-3.5932-14.4202-17.7444
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 340
2X-RAY DIFFRACTION2B4 - 340
3X-RAY DIFFRACTION3C4 - 340
4X-RAY DIFFRACTION4D4 - 340

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