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- PDB-4moz: Fructose-bisphosphate aldolase from Slackia heliotrinireducens DS... -

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Basic information

Entry
Database: PDB / ID: 4moz
TitleFructose-bisphosphate aldolase from Slackia heliotrinireducens DSM 20476
ComponentsFructose-bisphosphate aldolase
KeywordsLYASE / PSI-Biology / MCSG / Midwest Center for Structural Genomics / fructose-bisphosphate aldolase
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity
Similarity search - Function
Aldolase FbaB-like, archaeal-type / : / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
fructose-bisphosphate aldolase
Similarity search - Component
Biological speciesSlackia heliotrinireducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsChang, C. / Li, H. / Jedrzejczak, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Fructose-bisphosphate aldolase from Slackia heliotrinireducens DSM 20476
Authors: Chang, C. / Li, H. / Jedrzejczak, R. / Joachimiak, A.
History
DepositionSep 12, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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
C: Fructose-bisphosphate aldolase
D: Fructose-bisphosphate aldolase
E: Fructose-bisphosphate aldolase


Theoretical massNumber of molelcules
Total (without water)173,0145
Polymers173,0145
Non-polymers00
Water20,0691114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15220 Å2
ΔGint-85 kcal/mol
Surface area51880 Å2
MethodPISA
2
A: Fructose-bisphosphate aldolase
B: Fructose-bisphosphate aldolase
C: Fructose-bisphosphate aldolase
D: Fructose-bisphosphate aldolase
E: Fructose-bisphosphate aldolase

A: Fructose-bisphosphate aldolase
B: Fructose-bisphosphate aldolase
C: Fructose-bisphosphate aldolase
D: Fructose-bisphosphate aldolase
E: Fructose-bisphosphate aldolase


Theoretical massNumber of molelcules
Total (without water)346,02810
Polymers346,02810
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_755-x+2,y,-z+1/21
Buried area35620 Å2
ΔGint-202 kcal/mol
Surface area98570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.783, 174.202, 203.023
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Fructose-bisphosphate aldolase


Mass: 34602.820 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Slackia heliotrinireducens (bacteria) / Strain: DSM 20476 / Gene: Shel_19790 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: C7N7V8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1114 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 90 mM HEPES, 1.26M Sodium Citrate, 10% Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 11, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 128812 / Num. obs: 128506 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.1 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 18
Reflection shellResolution: 2.15→2.17 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.765 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3136 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
SBC-CollectCOLLECTdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
ARP/wARPmodel building
RESOLVEphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0 / SU B: 10.352 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.744 / ESU R Free: 0.162
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2232 6390 5 %RANDOM
Rwork0.1688 ---
obs0.1715 127017 98.01 %-
all-127017 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 111.63 Å2 / Biso mean: 33.0525 Å2 / Biso min: 15.05 Å2
Baniso -1Baniso -2Baniso -3
1-3.21 Å20 Å20 Å2
2---3.33 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11830 0 0 1114 12944
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0212138
X-RAY DIFFRACTIONr_angle_refined_deg0.9551.95516496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.01851598
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.95425.074544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.567151957
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.4881560
X-RAY DIFFRACTIONr_chiral_restr0.0680.21884
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0219289
X-RAY DIFFRACTIONr_rigid_bond_restr1.478312138
X-RAY DIFFRACTIONr_sphericity_free30.9195348
X-RAY DIFFRACTIONr_sphericity_bonded12.222512692
LS refinement shellResolution: 2.154→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 415 -
Rwork0.232 7778 -
all-8193 -
obs-8193 88.92 %

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