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- PDB-3bv4: Crystal structure of a rabbit muscle fructose-1,6-bisphosphate al... -

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Basic information

Entry
Database: PDB / ID: 3bv4
TitleCrystal structure of a rabbit muscle fructose-1,6-bisphosphate aldolase A dimer variant
ComponentsFructose-bisphosphate aldolase A
KeywordsLYASE / Acetylation / Glycolysis / Phosphoprotein / Schiff base
Function / homology
Function and homology information


negative regulation of Arp2/3 complex-mediated actin nucleation / fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / M band / I band / glycolytic process / protein homotetramerization / positive regulation of cell migration
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
1,3-DIHYDROXYACETONEPHOSPHATE / Fructose-bisphosphate aldolase A
Similarity search - Component
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsSherawat, M. / Tolan, D.R. / Allen, K.N.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Structure of a rabbit muscle fructose-1,6-bisphosphate aldolase A dimer variant.
Authors: Sherawat, M. / Tolan, D.R. / Allen, K.N.
History
DepositionJan 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,7988
Polymers37,0511
Non-polymers7467
Water6,107339
1
A: Fructose-bisphosphate aldolase A
hetero molecules

A: Fructose-bisphosphate aldolase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,59616
Polymers74,1032
Non-polymers1,49314
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.320, 137.900, 51.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-3505-

HOH

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Components

#1: Protein Fructose-bisphosphate aldolase A / Muscle-type aldolase


Mass: 37051.391 Da / Num. of mol.: 1 / Mutation: D128V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: ALDOA / Plasmid: pPB1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83 / References: UniProt: P00883, fructose-bisphosphate aldolase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-13P / 1,3-DIHYDROXYACETONEPHOSPHATE


Mass: 170.058 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 339 / 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: 2.54 Å3/Da / Density % sol: 51.53 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.1
Details: 0.2 M ammonium sulfate, 25% PEG 2K monomethyl ether, 100 mM sodium acetate, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2006 / Details: mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. all: 41975 / Num. obs: 41975 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Χ2: 1.561 / Net I/σ(I): 20.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 7.3 / Num. unique all: 4177 / Rsym value: 7.3 / Χ2: 1.668 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
PDB_EXTRACT3.004data extraction
CBASSdata collection
AMoREphasing
RefinementStarting model: pdb entry 1ALD

1ald


Resolution: 1.7→19.51 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1463854.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 4071 10.1 %RANDOM
Rwork0.192 ---
obs0.192 40471 95.5 %-
all-40471 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.636 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso mean: 18.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å20 Å20 Å2
2---0.74 Å20 Å2
3---1.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.7→19.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 40 339 2980
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d3.02
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.832
X-RAY DIFFRACTIONc_scbond_it2.082
X-RAY DIFFRACTIONc_scangle_it3.022.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.235 591 9.3 %
Rwork0.214 5771 -
all-6362 -
obs--91.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4g3h.paramg3h.top

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