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- PDB-5ud2: Class II fructose-1,6-bisphosphate aldolase H180Q variant of Heli... -

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Basic information

Entry
Database: PDB / ID: 5ud2
TitleClass II fructose-1,6-bisphosphate aldolase H180Q variant of Helicobacter pylori with DHAP
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 / Fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.775 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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
B: Fructose-bisphosphate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,22910
Polymers67,5822
Non-polymers6488
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5170 Å2
ΔGint-201 kcal/mol
Surface area22080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.407, 63.089, 64.789
Angle α, β, γ (deg.)82.51, 75.96, 74.39
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-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.: 396 / 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: 2.22 Å3/Da / Density % sol: 44.63 %
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: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.775→35.785 Å / Num. obs: 50414 / % possible obs: 83.39 % / Redundancy: 2.1 % / Net I/σ(I): 7.83

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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: 1.775→35.785 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0.04 / Phase error: 24.32
RfactorNum. reflection% reflection
Rfree0.2159 2313 4.94 %
Rwork0.193 --
obs0.1942 46853 83.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.775→35.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4516 0 26 396 4938
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044708
X-RAY DIFFRACTIONf_angle_d0.5966344
X-RAY DIFFRACTIONf_dihedral_angle_d15.0482860
X-RAY DIFFRACTIONf_chiral_restr0.041698
X-RAY DIFFRACTIONf_plane_restr0.003830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7748-1.8110.2774740.28171352X-RAY DIFFRACTION43
1.811-1.85040.3155930.28311731X-RAY DIFFRACTION55
1.8504-1.89340.3255920.26421855X-RAY DIFFRACTION60
1.8934-1.94070.30121020.25392124X-RAY DIFFRACTION67
1.9407-1.99320.28751300.25672315X-RAY DIFFRACTION74
1.9932-2.05190.29061320.24112572X-RAY DIFFRACTION82
2.0519-2.11810.28481370.22292715X-RAY DIFFRACTION86
2.1181-2.19380.2411600.20962810X-RAY DIFFRACTION89
2.1938-2.28160.22771470.20572896X-RAY DIFFRACTION92
2.2816-2.38540.23451430.20362914X-RAY DIFFRACTION93
2.3854-2.51110.25291580.19472958X-RAY DIFFRACTION94
2.5111-2.66840.25631580.19762965X-RAY DIFFRACTION95
2.6684-2.87440.20551550.18663028X-RAY DIFFRACTION96
2.8744-3.16350.22741530.19543037X-RAY DIFFRACTION97
3.1635-3.62090.1751570.17723082X-RAY DIFFRACTION97
3.6209-4.56040.15411600.14743080X-RAY DIFFRACTION98
4.5604-35.79220.1571620.1593106X-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)
10.0020.0002-0.00150.001-0.00190.0038-0.002-0.0228-0.01010.00230.0119-0.01160.01190.005900.10340.0311-0.00120.1857-0.03320.10271.646620.2973-14.1006
20.04510.02120.03280.0439-0.01750.0525-0.028-0.15430.062-0.04420.02360.00130.02630.0382-0.00560.07130.01220.0050.1093-0.01930.0876-9.420419.406-22.8115
30.01940.0001-0.0220.01170.00860.02950.0214-0.07730.06920.01510.0136-0.0117-0.0021-0.02360.01390.0920.0228-0.00380.1588-0.05110.1139-10.624334.0598-13.7713
40.0019-0.0030.00360.0176-0.01040.02320.0044-0.06050.0724-0.00910.08340.0059-0.06550.00760.01130.0891-0.0030.01580.1395-0.07460.1454-3.018839.101-19.0185
50.3498-0.1404-0.08960.1030.04920.0715-0.0446-0.08030.0989-0.15720.0939-0.091-0.11780.09250.04690.149-0.1130.03790.01730.00690.07350.040428.6012-37.7661
60.00140.00120.00130.0049-0.00490.00950.01160.0141-0.0227-0.00460.02130.02030.0128-0.02890.00220.0508-0.00580.01620.102-0.04060.1557-19.5166-12.0768-45.0816
70.01070.02110.0040.07-0.03340.0551-0.02320.0543-0.07680.02790.01210.0206-0.03390.0268-0.00070.05840.00330.0060.0644-0.00550.0816-8.2978-3.2413-44.4777
80.0052-0.0053-0.00090.00340.00340.00530.00550.0335-0.0694-0.0401-0.0033-0.01940.0183-0.00320.00190.07340.00890.01770.1123-0.04780.1489-5.9904-16.8147-58.6159
90.0198-0.01210.00760.0144-0.00430.00300.0489-0.0408-0.0753-0.0616-0.052-0.0105-0.0121-0.0180.1230.00130.00270.1315-0.06690.14-12.984-7.2154-62.4145
100.1925-0.0018-0.01190.0285-0.00050.00230.04570.1065-0.0857-0.0526-0.01630.0261-0.0468-0.03830.01080.13310.02-0.0470.09760.01360.0687-17.62345.9752-61.4223
110.0343-0.0207-0.01250.01290.00960.1022-0.025-0.0006-0.01030.00960.00740.0504-0.1793-0.0594-0.04980.19180.0438-0.06670.03310.02790.0823-18.085515.1838-49.0617
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 127 )
3X-RAY DIFFRACTION3chain 'A' and (resid 128 through 184 )
4X-RAY DIFFRACTION4chain 'A' and (resid 185 through 216 )
5X-RAY DIFFRACTION5chain 'A' and (resid 217 through 307 )
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 15 )
7X-RAY DIFFRACTION7chain 'B' and (resid 16 through 127 )
8X-RAY DIFFRACTION8chain 'B' and (resid 128 through 167 )
9X-RAY DIFFRACTION9chain 'B' and (resid 168 through 216 )
10X-RAY DIFFRACTION10chain 'B' and (resid 217 through 255 )
11X-RAY DIFFRACTION11chain 'B' and (resid 256 through 307 )

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