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- PDB-2ekc: Structural study of Project ID aq_1548 from Aquifex aeolicus VF5 -

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Basic information

Entry
Database: PDB / ID: 2ekc
TitleStructural study of Project ID aq_1548 from Aquifex aeolicus VF5
ComponentsTryptophan synthase alpha chain
KeywordsLYASE / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / cytosol
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsAsada, Y. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structural study of Project ID aq_1548 from Aquifex aeolicus VF5
Authors: Asada, Y. / Kunishima, N.
History
DepositionMar 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan synthase alpha chain
B: Tryptophan synthase alpha chain


Theoretical massNumber of molelcules
Total (without water)59,0932
Polymers59,0932
Non-polymers00
Water11,061614
1
A: Tryptophan synthase alpha chain


Theoretical massNumber of molelcules
Total (without water)29,5461
Polymers29,5461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tryptophan synthase alpha chain


Theoretical massNumber of molelcules
Total (without water)29,5461
Polymers29,5461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.854, 72.985, 64.942
Angle α, β, γ (deg.)90.000, 90.697, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tryptophan synthase alpha chain / aq_1548


Mass: 29546.354 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 CodonPlus(DE3)-RIL / References: UniProt: O67502, tryptophan synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 614 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 46.96 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.1
Details: 30v/v(%) PEG 200, 0.1M MES, 5w/v(%) PEG 3K, pH 6.1, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 11, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 36575 / Num. obs: 36575 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 19.938 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 10
Reflection shellResolution: 2→2.07 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 4.17 / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.67 Å / Isotropic thermal model: RESTRAINED / Cross valid method: TROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1812 -RAMDOM
Rwork0.184 ---
all0.186 36501 --
obs0.186 36501 99.5 %-
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.89 Å20 Å21.04 Å2
2---2.56 Å20 Å2
3----1.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→29.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4054 0 0 614 4668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.016
RfactorNum. reflection% reflection
Rfree0.251 244 -
Rwork0.202 --
obs--99.8 %

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