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- PDB-2iqt: Crystal Structure of Fructose-Bisphosphate Aldolase, Class I from... -

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Basic information

Entry
Database: PDB / ID: 2iqt
TitleCrystal Structure of Fructose-Bisphosphate Aldolase, Class I from Porphyromonas gingivalis
ComponentsFructose-bisphosphate aldolase class 1
KeywordsLYASE / TIM berrel / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


fructose-bisphosphate aldolase / fructose-bisphosphate aldolase activity / glycolytic process
Similarity search - Function
Fructose-bisphosphate aldolase class I, Gram-positive bacteria-type / 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
Fructose-bisphosphate aldolase class 1
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.46 Å
AuthorsKim, Y. / Zhou, M. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Fructose-Bisphosphate Aldolase, Class I from Porphyromonas gingivalis
Authors: Kim, Y. / Zhou, M. / Moy, S. / Joachimiak, A.
History
DepositionOct 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fructose-bisphosphate aldolase class 1


Theoretical massNumber of molelcules
Total (without water)33,9571
Polymers33,9571
Non-polymers00
Water2,306128
1
A: Fructose-bisphosphate aldolase class 1

A: Fructose-bisphosphate aldolase class 1


Theoretical massNumber of molelcules
Total (without water)67,9142
Polymers67,9142
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Unit cell
Length a, b, c (Å)68.737, 68.737, 154.113
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-307-

HOH

21A-359-

HOH

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Components

#1: Protein Fructose-bisphosphate aldolase class 1 / Fructose-biphosphate aldolase class I / FBP aldolase


Mass: 33956.910 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: fbaB / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: P60053, fructose-bisphosphate aldolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.2 M Ammonium citrate tribasic, 100 mM BTP, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97869
DetectorType: SBC-3 / Detector: CCD / Date: Dec 17, 2005 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 2.44→38.89 Å / Num. all: 16237 / Num. obs: 16237 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.5 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 7
Reflection shellResolution: 2.44→2.53 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 3.8 / Num. unique all: 1602 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
SOLVEphasing
RESOLVEphasing
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.46→38.89 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 14.105 / SU ML: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.371 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23172 1612 10.1 %RANDOM
Rwork0.18167 ---
all0.18686 14343 --
obs0.18686 14343 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.452 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å20 Å2
2--0.51 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.46→38.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2326 0 0 128 2454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222510
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5171.9693400
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225322
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.85425.164122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.10415478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4151516
X-RAY DIFFRACTIONr_chiral_restr0.1080.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021938
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2260.21326
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2158
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3220.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8061.51613
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.2422519
X-RAY DIFFRACTIONr_scbond_it2.35231015
X-RAY DIFFRACTIONr_scangle_it3.84.5881
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.457→2.521 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.287 112
Rwork0.213 1034
obs-1034
Refinement TLS params.Method: refined / Origin x: 26.4417 Å / Origin y: 31.1258 Å / Origin z: 61.6001 Å
111213212223313233
T-0.0835 Å20.0096 Å20.0038 Å2-0.0036 Å2-0.0217 Å2---0.0552 Å2
L0.3703 °2-0.0435 °2-0.2977 °2-0.4149 °20.1836 °2--0.6291 °2
S0.0048 Å °0.0502 Å °-0.0083 Å °0.0025 Å °-0.033 Å °0.0144 Å °-0.0044 Å °0.023 Å °0.0283 Å °

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