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- PDB-1ok4: Archaeal fructose 1,6-bisphosphate aldolase covalently bound to t... -

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Basic information

Entry
Database: PDB / ID: 1ok4
TitleArchaeal fructose 1,6-bisphosphate aldolase covalently bound to the substrate dihydroxyacetone phosphate
ComponentsFRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
KeywordsLYASE / ALDOLASE / FRUCTOSE 1 / 6-BISPHOSPHATE / TIM BARREL / GLYCOLYTIC / ARCHAEAL
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process / cytoplasm
Similarity search - Function
Aldolase FbaB-like, archaeal-type / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / DeoC/LacD family aldolase / 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 1
Similarity search - Component
Biological speciesTHERMOPROTEUS TENAX (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLorentzen, E. / Zwart, P. / Stark, A. / Hensel, R. / Siebers, B. / Pohl, E.
CitationJournal: J. Biol. Chem. / Year: 2003
Title: Crystal structure of an archaeal class I aldolase and the evolution of (betaalpha)8 barrel proteins.
Authors: Lorentzen, E. / Pohl, E. / Zwart, P. / Stark, A. / Russell, R.B. / Knura, T. / Hensel, R. / Siebers, B.
History
DepositionJul 17, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 4, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" "BA" "CA" IN EACH CHAIN ON SHEET ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" "BA" "CA" IN EACH CHAIN ON SHEET RECORD BELOW ARE ACTUALLY 9-STRANDED BARRELS THESE ARE REPRESENTED BY 10-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" "EA" "FA" "GA" "HA" "IA" "JA" IN EACH CHAIN ON SHEET RECORDS BELOW ARE ACTUALLY 7-STRANDED BARRELS THESE ARE REPRESENTED BY 8-STRANDED SHEETS IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
B: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
C: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
D: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
E: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
F: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
G: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
H: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
I: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
J: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)289,11120
Polymers287,41110
Non-polymers1,70110
Water11,548641
1
A: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
B: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
C: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
D: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
E: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,55610
Polymers143,7055
Non-polymers8505
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
F: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
G: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
H: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
I: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
J: FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,55610
Polymers143,7055
Non-polymers8505
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)82.400, 157.300, 101.500
Angle α, β, γ (deg.)90.00, 108.20, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A3 - 24
2112B3 - 24
3112C3 - 24
4112D3 - 24
5112E3 - 24
6112F3 - 24
7112G3 - 24
8112H3 - 24
9112I3 - 24
10112J3 - 24
1212A30 - 43
2212B30 - 43
3212C30 - 43
4212D30 - 43
5212E30 - 43
6212F30 - 43
7212G30 - 43
8212H30 - 43
9212I30 - 43
10212J30 - 43
1312A52 - 86
2312B52 - 86
3312C52 - 86
4312D52 - 86
5312E52 - 86
6312F52 - 86
7312G52 - 86
8312H52 - 86
9312I52 - 86
10312J52 - 86
1412A88 - 131
2412B88 - 131
3412C88 - 131
4412D88 - 131
5412E88 - 131
6412F88 - 131
7412G88 - 131
8412H88 - 131
9412I88 - 131
10412J88 - 131
1512A133 - 151
2512B133 - 151
3512C133 - 151
4512D133 - 151
5512E133 - 151
6512F133 - 151
7512G133 - 151
8512H133 - 151
9512I133 - 151
10512J133 - 151
1612A156 - 210
2612B156 - 210
3612C156 - 210
4612D156 - 210
5612E156 - 210
6612F156 - 210
7612G156 - 210
8612H156 - 210
9612I156 - 210
10612J156 - 210
1712A223 - 237
2712B223 - 237
3712C223 - 237
4712D223 - 237
5712E223 - 237
6712F223 - 237
7712G223 - 237
8712H223 - 237
9712I223 - 237
10712J223 - 237
1812A239 - 251
2812B239 - 251
3812C239 - 251
4812D239 - 251
5812E239 - 251
6812F239 - 251
7812G239 - 251
8812H239 - 251
9812I239 - 251
10812J239 - 251

NCS oper: (Code: given
Matrix: (0.96895, -0.16745, -0.18194), (-0.11733, 0.33637, -0.93439), (0.21767, 0.92672, 0.30628)
Vector: 21.34281, 90.45076, -70.82803)

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Components

#1: Protein
FRUCTOSE-BISPHOSPHATE ALDOLASE CLASS I / FBP ALDOLASE


Mass: 28741.064 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Details: LYS177 SCHIFF-BASE WITH DHAP / Source: (gene. exp.) THERMOPROTEUS TENAX (unknown) / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (unknown) / References: UniProt: P58315, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE / Dihydroxyacetone phosphate


Mass: 170.058 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H7O6P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 641 / Source method: isolated from a natural source / Formula: H2O
Compound detailsLYSINE 177 FORMS A SCHIFF-BASE WITH DIHYDROXYACETONE PHOSPHATE SUBSTRATE. ASP 24 IS THE GENERAL ...LYSINE 177 FORMS A SCHIFF-BASE WITH DIHYDROXYACETONE PHOSPHATE SUBSTRATE. ASP 24 IS THE GENERAL BASE, TYR 146 IS THE PROTON DONOR.

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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: 45 %
Crystal growpH: 5
Details: 9% (W/V) PEG 4000, 0.1 M NA ACETATE PH 5.0, 1-8% GLYCEROL, 100 MM DHAP
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
13 mg/mlprotein1drop
210 mMHEPES-NaOH1droppH7.5
3100 mM1dropKCl
41 mMdithiothreitol1drop
59 %(w/v)PEG40001reservoir
60.1 Msodium acetate1reservoirpH5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.845
DetectorDate: Feb 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.845 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 125363 / % possible obs: 90.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 13.6
Reflection shellResolution: 2.1→2.19 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.3 / % possible all: 59.3
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 40 Å / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
% possible obs: 59.3 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 2.3

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1OJX
Resolution: 2.1→36.51 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.797 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.231 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.185 3203 2.5 %RANDOM
Rwork0.163 ---
obs0.164 125363 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.07 Å2
2---0.12 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19358 0 90 641 20089
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02219878
X-RAY DIFFRACTIONr_bond_other_d0.0030.0218456
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9726890
X-RAY DIFFRACTIONr_angle_other_deg0.834342784
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.66652492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0790.22930
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0222114
X-RAY DIFFRACTIONr_gen_planes_other0.0030.024162
X-RAY DIFFRACTIONr_nbd_refined0.2020.23982
X-RAY DIFFRACTIONr_nbd_other0.2390.220513
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.210681
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2802
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3270.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.370.264
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2550.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6031.512378
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.295219780
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.19937500
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9164.57110
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3226 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Atight positional0.030.05
2Btight positional0.030.05
3Ctight positional0.020.05
4Dtight positional0.020.05
5Etight positional0.030.05
6Ftight positional0.020.05
7Gtight positional0.030.05
8Htight positional0.030.05
9Itight positional0.020.05
10Jtight positional0.030.05
1Atight thermal0.090.5
2Btight thermal0.110.5
3Ctight thermal0.090.5
4Dtight thermal0.080.5
5Etight thermal0.10.5
6Ftight thermal0.090.5
7Gtight thermal0.10.5
8Htight thermal0.10.5
9Itight thermal0.090.5
10Jtight thermal0.10.5
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.26 158
Rwork0.249 5639
Refinement
*PLUS
Lowest resolution: 40 Å / Rfactor Rfree: 0.187 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.013
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3

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