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- PDB-5uck: Class II fructose-1,6-bisphosphate aldolase of Helicobacter pylor... -

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Basic information

Entry
Database: PDB / ID: 5uck
TitleClass II fructose-1,6-bisphosphate aldolase of Helicobacter pylori with cleavage products
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
1,3-DIHYDROXYACETONEPHOSPHATE / GLYCERALDEHYDE-3-PHOSPHATE / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.782 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 22, 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 / 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.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)68,58912
Polymers67,6022
Non-polymers98810
Water6,864381
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6260 Å2
ΔGint-210 kcal/mol
Surface area21580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.384, 62.843, 64.754
Angle α, β, γ (deg.)82.23, 75.97, 74.40
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 33800.812 Da / Num. of mol.: 2
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

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Non-polymers , 5 types, 391 molecules

#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-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O6P
#5: Chemical ChemComp-G3H / GLYCERALDEHYDE-3-PHOSPHATE


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


Mass: 18.015 Da / Num. of mol.: 381 / 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: 44.32 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 1000, PEG 8000, Calcium acetate, Tris-Acetic acid buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.782→45.19 Å / Num. obs: 51940 / % possible obs: 85.29 % / Redundancy: 1.9 % / Biso Wilson estimate: 19 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.0586 / Net I/σ(I): 9.02
Reflection shellResolution: 1.782→1.846 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.4454 / Mean I/σ(I) obs: 1.26 / CC1/2: 0.783 / % possible all: 60.81

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Processing

Software
NameVersionClassification
PHENIX(dev_2481)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3C4U

3c4u


Resolution: 1.782→45.19 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 29.79
RfactorNum. reflection% reflection
Rfree0.2319 2284 4.85 %
Rwork0.1907 --
obs0.1928 47109 85.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.48 Å2
Refinement stepCycle: LAST / Resolution: 1.782→45.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4495 0 46 381 4922
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044703
X-RAY DIFFRACTIONf_angle_d0.716333
X-RAY DIFFRACTIONf_dihedral_angle_d12.4052845
X-RAY DIFFRACTIONf_chiral_restr0.042694
X-RAY DIFFRACTIONf_plane_restr0.003823
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7819-1.82060.4175900.3211799X-RAY DIFFRACTION55
1.8206-1.8630.35391280.31062303X-RAY DIFFRACTION70
1.863-1.90960.34271010.31132337X-RAY DIFFRACTION71
1.9096-1.96120.351340.29632443X-RAY DIFFRACTION74
1.9612-2.01890.30931410.26132623X-RAY DIFFRACTION80
2.0189-2.08410.31771300.24882697X-RAY DIFFRACTION81
2.0841-2.15860.25961450.21562852X-RAY DIFFRACTION87
2.1586-2.2450.24651510.19562892X-RAY DIFFRACTION89
2.245-2.34720.21811530.19082910X-RAY DIFFRACTION89
2.3472-2.47090.27321500.19453089X-RAY DIFFRACTION93
2.4709-2.62570.25631540.19893058X-RAY DIFFRACTION93
2.6257-2.82840.2571600.18773078X-RAY DIFFRACTION94
2.8284-3.1130.22641600.19363114X-RAY DIFFRACTION96
3.113-3.56330.20551550.16763210X-RAY DIFFRACTION97
3.5633-4.48870.17181700.14933172X-RAY DIFFRACTION97
4.4887-45.20620.18241620.15633248X-RAY DIFFRACTION99
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)
10.0039-0.00430.00120.0037-0.00410.0080.0342-0.0455-0.0220.03110.0095-0.0111-0.03720.0382-00.12980.0199-0.02280.2837-0.08770.25091.988119.4173-14.4275
20.04540.04210.04660.10260.03440.1023-0.0215-0.14460.1094-0.05790.04150.0005-0.04160.0202-00.14340.0172-0.00140.2335-0.07120.2237-9.40422.409-20.8925
30.4617-0.1111-0.12970.09690.01980.0992-0.0679-0.08860.3293-0.26140.2036-0.0344-0.21620.1650.06340.2658-0.08210.01130.12630.00570.1688-0.413830.5979-33.2653
40.00390.0014-0.00030.0073-0.00170.00050.025-0.0176-0.0141-0.0309-0.00370.02960.0219-0.023100.1293-0.01880.02680.2396-0.07570.3623-18.9265-12.8734-45.214
50.1042-0.00490.09080.11270.02480.1274-0.0040.1035-0.1049-0.0433-0.03320.0044-0.03720.0176-0.00120.12960.00210.0150.189-0.0580.2242-8.8968-6.8266-51.1863
60.2185-0.0777-0.00250.0649-0.00870.064-0.01760.2373-0.1123-0.1089-0.10340.0701-0.2467-0.123-0.11570.22340.019-0.07250.06970.07750.0569-17.417810.8-54.3046
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 184 )
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 307 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 15 )
5X-RAY DIFFRACTION5chain 'B' and (resid 16 through 216 )
6X-RAY DIFFRACTION6chain 'B' and (resid 217 through 307 )

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