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- PDB-5vjd: Class II fructose-1,6-bisphosphate aldolase of Escherichia coli w... -

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Basic information

Entry
Database: PDB / ID: 5vjd
TitleClass II fructose-1,6-bisphosphate aldolase of Escherichia coli with DHAP
ComponentsFructose-bisphosphate aldolase class 2
KeywordsLYASE / Glycolysis
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / gluconeogenesis / glycolytic process / protein homodimerization activity / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
Fructose-bisphosphate aldolase, class II, yeast/E. coli subtype / 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
1,3-DIHYDROXYACETONEPHOSPHATE / Fructose-bisphosphate aldolase class 2
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.701 Å
AuthorsSygusch, J. / Coincon, M.
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
DepositionApr 19, 2017Deposition 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_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 class 2
B: Fructose-bisphosphate aldolase class 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,68310
Polymers78,1202
Non-polymers5638
Water17,493971
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6500 Å2
ΔGint-144 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.174, 71.454, 88.185
Angle α, β, γ (deg.)90.00, 108.94, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Fructose-bisphosphate aldolase class 2 / FBPA / Fructose-1 / 6-bisphosphate aldolase / Fructose-bisphosphate aldolase class II


Mass: 39059.957 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fbaA, fba, fda, b2925, JW2892 / Production host: Escherichia coli (E. coli) / References: UniProt: P0AB71, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 971 / 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: 2.18 Å3/Da / Density % sol: 43.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 4000, MgCl2, Hepes buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.701→39.871 Å / Num. obs: 72711 / % possible obs: 99 % / Redundancy: 3.5 % / Biso Wilson estimate: 14.9 Å2 / Rsym value: 0.08 / Net I/σ(I): 19

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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: 1B57

1b57


Resolution: 1.701→39.871 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1725 2977 4.1 %
Rwork0.1475 --
obs0.1485 72643 98.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.701→39.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5284 0 26 971 6281
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045457
X-RAY DIFFRACTIONf_angle_d0.7157407
X-RAY DIFFRACTIONf_dihedral_angle_d16.3043237
X-RAY DIFFRACTIONf_chiral_restr0.045818
X-RAY DIFFRACTIONf_plane_restr0.004959
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7012-1.72910.33361190.32612762X-RAY DIFFRACTION82
1.7291-1.75890.29171380.30213276X-RAY DIFFRACTION98
1.7589-1.79090.2951390.25713303X-RAY DIFFRACTION99
1.7909-1.82530.23771380.23873289X-RAY DIFFRACTION99
1.8253-1.86260.26221410.22633325X-RAY DIFFRACTION99
1.8626-1.90310.22491430.20523347X-RAY DIFFRACTION99
1.9031-1.94740.22511410.19353299X-RAY DIFFRACTION99
1.9474-1.99610.17741410.17153341X-RAY DIFFRACTION99
1.9961-2.050.18841460.15793340X-RAY DIFFRACTION99
2.05-2.11040.1921420.14513307X-RAY DIFFRACTION100
2.1104-2.17850.16971420.13423371X-RAY DIFFRACTION99
2.1785-2.25630.16281410.13413310X-RAY DIFFRACTION99
2.2563-2.34670.14521470.12543337X-RAY DIFFRACTION100
2.3467-2.45340.14771440.12263386X-RAY DIFFRACTION100
2.4534-2.58280.15091460.12633372X-RAY DIFFRACTION100
2.5828-2.74450.17561400.13353347X-RAY DIFFRACTION100
2.7445-2.95640.16081450.13293378X-RAY DIFFRACTION100
2.9564-3.25380.16051470.12743381X-RAY DIFFRACTION100
3.2538-3.72430.13821490.12173367X-RAY DIFFRACTION100
3.7243-4.69110.13261420.11323406X-RAY DIFFRACTION100
4.6911-39.88230.17661460.14993422X-RAY DIFFRACTION98
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)
10.60480.4463-0.12380.4708-0.09330.46830.0692-0.08460.01910.1181-0.09050.0105-0.0330.06-0.00740.114-0.0207-0.00690.11740.00720.11259.6107-10.906121.6874
20.0841-0.0332-0.09280.09440.00360.18170.0245-0.05820.0882-0.03230.04760.1363-0.1479-0.0160.00670.1646-0.0317-0.01990.18010.09160.301612.76474.74468.501
30.34190.02540.0966-0.0308-0.00580.088-0.02470.09350.0352-0.0285-0.00330.0055-0.0090.0207-0.01340.1049-0.00520.00050.13820.01110.1277-3.2704-15.32415.2644
40.17340.08030.00710.4591-0.26080.10270.0133-0.0392-0.02640.0263-0.0069-0.03190.0119-0.007500.122600.00320.11180.01010.1051-14.5244-31.620529.8378
50.12820.058-0.14220.1263-0.22230.1891-0.003-0.0382-0.0229-0.0201-0.0046-0.08620.02450.040500.13050.00350.00040.11210.0110.1247-5.3401-35.487127.0264
60.10980.0097-0.05520.0746-0.10060.0635-0.04150.0072-0.0615-0.0923-0.0117-0.06770.12760.076-0.00580.19640.00290.010.11320.01010.1521-9.1522-49.134727.7064
70.08060.0082-0.11740.11490.02180.09570.0053-0.0417-0.0661-0.1033-0.0623-0.05830.1254-0.0472-0.00880.2004-0.0293-0.01830.14070.01410.145-19.1293-51.550629.5965
80.1918-0.0936-0.10180.15110.12980.0844-0.08320.199-0.0597-0.21060.11080.17270.1296-0.1001-0.05670.2472-0.1034-0.07180.27830.04570.1637-30.9615-47.123225.0875
90.0326-0.01810.01190.0364-0.05490.11610.0037-0.0270.0397-0.01770.05620.10320.041-0.1134-0.00010.1214-0.0118-0.00180.14880.01750.1186-26.1122-31.529622.2131
100.02560.0160.0040.05930.02260.00660.09890.14350.34180.0555-0.176-0.123-0.06650.0032-0.00130.15670.0231-0.00510.15650.08370.219-13.9613-2.15775.2787
110.0757-0.09420.07190.0465-0.09360.0626-0.0199-0.00260.01720.02970.01240.0067-0.04-0.0654-00.11370.00590.01360.1160.00680.1196-22.8443-21.738124.9968
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 220 )
2X-RAY DIFFRACTION2chain 'A' and (resid 221 through 252 )
3X-RAY DIFFRACTION3chain 'A' and (resid 253 through 358 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 79 )
5X-RAY DIFFRACTION5chain 'B' and (resid 80 through 133 )
6X-RAY DIFFRACTION6chain 'B' and (resid 134 through 167 )
7X-RAY DIFFRACTION7chain 'B' and (resid 168 through 220 )
8X-RAY DIFFRACTION8chain 'B' and (resid 221 through 252 )
9X-RAY DIFFRACTION9chain 'B' and (resid 253 through 309 )
10X-RAY DIFFRACTION10chain 'B' and (resid 310 through 329 )
11X-RAY DIFFRACTION11chain 'B' and (resid 330 through 358 )

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