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

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Basic information

Entry
Database: PDB / ID: 6rng
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
GLYCINE / PROLINE / Fructose-bisphosphate aldolase 6, cytosolic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsShahar, A. / Zarivach, R. / Skirycz, A. / Wojciechowska, I.
CitationJournal: Not 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 8, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation / Item: _citation.journal_abbrev
Revision 1.2Jan 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

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase 6, cytosolic
B: Fructose-bisphosphate aldolase 6, cytosolic
F: Fructose-bisphosphate aldolase 6, cytosolic
G: Fructose-bisphosphate aldolase 6, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,55423
Polymers153,7354
Non-polymers1,81919
Water7,548419
1
B: Fructose-bisphosphate aldolase 6, cytosolic
hetero molecules

B: Fructose-bisphosphate aldolase 6, cytosolic
hetero molecules

A: Fructose-bisphosphate aldolase 6, cytosolic
hetero molecules

A: Fructose-bisphosphate aldolase 6, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,46022
Polymers153,7354
Non-polymers1,72518
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
crystal symmetry operation1_545x,y-1,z1
crystal symmetry operation2_545-x,y-1,-z1
Buried area9610 Å2
ΔGint-222 kcal/mol
Surface area46960 Å2
MethodPISA
2
F: Fructose-bisphosphate aldolase 6, cytosolic
hetero molecules

F: Fructose-bisphosphate aldolase 6, cytosolic
hetero molecules

G: Fructose-bisphosphate aldolase 6, cytosolic
hetero molecules

G: Fructose-bisphosphate aldolase 6, cytosolic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,64924
Polymers153,7354
Non-polymers1,91420
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_554-x,y,-z-11
crystal symmetry operation1_565x,y+1,z1
crystal symmetry operation2_564-x,y+1,-z-11
Buried area9450 Å2
ΔGint-203 kcal/mol
Surface area47150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.399, 73.164, 176.225
Angle α, β, γ (deg.)90.00, 106.52, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-599-

HOH

21F-614-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22F
13A
23G
14B
24F
15B
25G
16F
26G

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYSAA6 - 3386 - 338
21SERSERLYSLYSBB6 - 3386 - 338
12PHEPHEASPASPAA4 - 3404 - 340
22PHEPHEASPASPFC4 - 3404 - 340
13SERSERLYSLYSAA6 - 3386 - 338
23SERSERLYSLYSGD6 - 3386 - 338
14SERSERLYSLYSBB6 - 3386 - 338
24SERSERLYSLYSFC6 - 3386 - 338
15SERSERGLYGLYBB6 - 3396 - 339
25SERSERGLYGLYGD6 - 3396 - 339
16SERSERLYSLYSFC6 - 3386 - 338
26SERSERLYSLYSGD6 - 3386 - 338

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.: 13 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H9NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.27 Å3/Da / Density % sol: 45.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium Sulfate, 0.1 M Bis-Tris pH 6.4, 30% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07227 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: 1.07227 Å / Relative weight: 1
ReflectionResolution: 2.15→46.23 Å / Num. obs: 69691 / % possible obs: 96.8 % / Redundancy: 3.6 % / Rpim(I) all: 0.088 / Net I/σ(I): 5
Reflection shellResolution: 2.15→2.23 Å / Num. unique obs: 3615

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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: 2.15→46.23 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.866 / SU B: 19.687 / SU ML: 0.245 / Cross valid method: THROUGHOUT / ESU R: 0.471 / ESU R Free: 0.297 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29646 3110 5.1 %RANDOM
Rwork0.24323 ---
obs0.24596 58283 81.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 24.164 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å2-0.15 Å2
2--0.55 Å20 Å2
3----0.59 Å2
Refinement stepCycle: 1 / Resolution: 2.15→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10140 0 65 419 10624
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01410409
X-RAY DIFFRACTIONr_bond_other_d0.0010.0179677
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.66314104
X-RAY DIFFRACTIONr_angle_other_deg0.9321.63622680
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.70351353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.06222.77473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.667151801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8451560
X-RAY DIFFRACTIONr_chiral_restr0.0730.21395
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211677
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021779
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_it0.8251.5325400
X-RAY DIFFRACTIONr_mcbond_other0.8171.5315399
X-RAY DIFFRACTIONr_mcangle_it1.4292.2876742
X-RAY DIFFRACTIONr_mcangle_other1.4292.2886743
X-RAY DIFFRACTIONr_scbond_it0.7691.6685009
X-RAY DIFFRACTIONr_scbond_other0.7691.6685009
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2592.4547357
X-RAY DIFFRACTIONr_long_range_B_refined4.04218.81411722
X-RAY DIFFRACTIONr_long_range_B_other4.04218.8211723
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)
11A104040.11
12B104040.11
21A107020.09
22F107020.09
31A103940.11
32G103940.11
41B105080.1
42F105080.1
51B107520.09
52G107520.09
61F104980.11
62G104980.11
LS refinement shellResolution: 2.154→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.247 15 -
Rwork0.338 350 -
obs--6.62 %
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)
10.8208-0.05820.42350.86-0.01161.0005-0.02090.10150.0195-0.1690.0111-0.10690.05790.12480.00980.0592-0.00310.04550.07410.00690.049411.661310.1897-17.0269
21.14620.2672-0.02061.15090.07270.64660.0074-0.1660.03840.24050.0164-0.0913-0.01120.0498-0.02380.05420.011-0.01920.0485-0.01410.02084.6788-22.993120.3631
31.38690.00720.32681.0728-0.03280.8362-0.043-0.192-0.04210.16690.01790.14670.0235-0.1170.0250.03720.00740.03650.03420.00810.041613.578219.8867-67.3258
41.24060.1214-0.17970.9757-0.08790.5952-0.05370.14670.0451-0.20720.09190.0825-0.0287-0.0393-0.03820.0538-0.0207-0.03010.02390.00970.05620.1798-13.2955-104.7967
500000000000000-00.0402000.040200.0402000
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 340
2X-RAY DIFFRACTION2B6 - 339
3X-RAY DIFFRACTION3F4 - 340
4X-RAY DIFFRACTION4G6 - 339

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