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- PDB-2irp: Crystal structure of the l-fuculose-1-phosphate aldolase (aq_1979... -

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Entry
Database: PDB / ID: 2irp
TitleCrystal structure of the l-fuculose-1-phosphate aldolase (aq_1979) from aquifex aeolicus VF5
ComponentsPutative aldolase class 2 protein aq_1979
KeywordsLYASE / aldolase / aldehyde / enzymatic mechanism / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


methylthioribulose 1-phosphate dehydratase / methylthioribulose 1-phosphate dehydratase activity / L-methionine salvage from S-adenosylmethionine / L-methionine salvage from methylthioadenosine / zinc ion binding / cytoplasm
Similarity search - Function
Methylthioribulose-1-phosphate dehydratase / L-fuculose-1-phosphate Aldolase / Class II aldolase/adducin N-terminal domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Methylthioribulose-1-phosphate dehydratase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsJeyakanthan, J. / Gayathri, D. / Yogavel, M. / Velmurugan, D. / Baba, S. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the l-fuculose-1-phosphate aldolase (aq_1979) from aquifex aeolicus VF5
Authors: Jeyakanthan, J. / Gayathri, D. / Yogavel, M. / Velmurugan, D. / Baba, S. / Ebihara, A. / Kuramitsu, S. / Shinkai, A. / Shiro, Y. / Yokoyama, S.
History
DepositionOct 16, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative aldolase class 2 protein aq_1979
B: Putative aldolase class 2 protein aq_1979
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5816
Polymers47,3542
Non-polymers2274
Water6,125340
1
A: Putative aldolase class 2 protein aq_1979
hetero molecules

A: Putative aldolase class 2 protein aq_1979
hetero molecules

A: Putative aldolase class 2 protein aq_1979
hetero molecules

A: Putative aldolase class 2 protein aq_1979
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,16112
Polymers94,7074
Non-polymers4548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area9020 Å2
ΔGint-109 kcal/mol
Surface area33850 Å2
MethodPISA, PQS
2
B: Putative aldolase class 2 protein aq_1979
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,7903
Polymers23,6771
Non-polymers1142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: Putative aldolase class 2 protein aq_1979
hetero molecules

A: Putative aldolase class 2 protein aq_1979
hetero molecules

A: Putative aldolase class 2 protein aq_1979
hetero molecules

A: Putative aldolase class 2 protein aq_1979
hetero molecules

B: Putative aldolase class 2 protein aq_1979
hetero molecules

B: Putative aldolase class 2 protein aq_1979
hetero molecules

B: Putative aldolase class 2 protein aq_1979
hetero molecules

B: Putative aldolase class 2 protein aq_1979
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,32324
Polymers189,4148
Non-polymers90916
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation5_454x-1/2,y+1/2,z-1/21
crystal symmetry operation6_654-x+3/2,-y+1/2,z-1/21
crystal symmetry operation7_544-y+1/2,x-1/2,z-1/21
crystal symmetry operation8_564y+1/2,-x+3/2,z-1/21
Buried area22180 Å2
ΔGint-136 kcal/mol
Surface area62600 Å2
MethodPISA
4
B: Putative aldolase class 2 protein aq_1979
hetero molecules

B: Putative aldolase class 2 protein aq_1979
hetero molecules

B: Putative aldolase class 2 protein aq_1979
hetero molecules

B: Putative aldolase class 2 protein aq_1979
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,16112
Polymers94,7074
Non-polymers4548
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation3_645-y+1,x-1,z1
crystal symmetry operation4_665y+1,-x+1,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.500, 102.500, 116.045
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4
Components on special symmetry positions
IDModelComponents
11A-1315-

HOH

21A-1356-

HOH

31B-1306-

HOH

41B-1336-

HOH

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Components

#1: Protein Putative aldolase class 2 protein aq_1979 / L-fuculose-1-phosphate aldolase


Mass: 23676.762 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Plasmid: PET21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Condon Plus (DE3)-RIl-x / References: UniProt: O67788, L-fuculose-phosphate aldolase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 3.22 Å3/Da / Density % sol: 61.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.1M HEPES, 55% PEG 200, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9788, 0.9793, 0.9000
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jul 7, 2006 / Details: RH Coated Bent-cyrindrical Mirror
RadiationMonochromator: SI 111 Double Crystal Monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97881
20.97931
30.91
ReflectionResolution: 2.3→50 Å / Num. all: 26703 / Num. obs: 22865 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.054 / Rsym value: 0.07
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.59 / Rsym value: 0.642 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→19.34 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 352366.07 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1106 4.8 %RANDOM
Rwork0.2 ---
obs0.2 22865 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 113.166 Å2 / ksol: 0.360583 e/Å3
Displacement parametersBiso mean: 53.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.8 Å20 Å20 Å2
2---0.8 Å20 Å2
3---1.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3280 0 10 340 3630
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.661.5
X-RAY DIFFRACTIONc_mcangle_it7.282
X-RAY DIFFRACTIONc_scbond_it8.432
X-RAY DIFFRACTIONc_scangle_it11.042.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.301 168 4.6 %
Rwork0.255 3450 -
obs--93.2 %
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 DIFFRACTION4BME.paramBME.top

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