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- PDB-1q7r: X-ray crystallographic analysis of a predicted amidotransferase f... -

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Basic information

Entry
Database: PDB / ID: 1q7r
TitleX-ray crystallographic analysis of a predicted amidotransferase from B. stearothermophilus at 1.9 A resolution
Componentspredicted amidotransferase
KeywordsTRANSFERASE / structural genomics / yaaE / pdx2 / predicted glutamine amidotransferase / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


pyridoxal 5'-phosphate synthase (glutamine hydrolysing) / pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity / pyridoxal phosphate biosynthetic process / glutamine catabolic process / glutaminase / glutaminase activity
Similarity search - Function
Pyridoxal 5'-phosphate synthase subunit PdxT/SNO / PdxT/SNO family, conserved site / SNO glutamine amidotransferase family / PdxT/SNO family family signature. / PdxT/SNO family profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Pyridoxal 5'-phosphate synthase subunit PdxT
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsMiller, D.J. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray structure analysis of a predicted amidotransferase from B. stearothermophilus at 1.9 A resolution
Authors: Miller, D.J. / Anderson, W.F.
History
DepositionAug 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999sequence No appropriate sequence database reference was available at the time of processing this file.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: predicted amidotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6334
Polymers24,4401
Non-polymers1943
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.947, 44.947, 202.668
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein predicted amidotransferase


Mass: 24439.818 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P83813
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / 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: 2.09 Å3/Da / Density % sol: 41.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: drop: 0.05 M NaAc pH 5.0, 5 mM Tris pH 8.3, 9% PEG 4K, 0.15 M AmS, 0.25 M NaCl, 2.5 mM DTT; resevoir: 0.1 M NaAc pH 5.0, 18 % PEG 4K, 0.3 M AmS., VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.979174 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 29, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979174 Å / Relative weight: 1
ReflectionResolution: 1.9→27 Å / Num. all: 16403 / Num. obs: 16323 / % possible obs: 93.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 5.5
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 2.6 / Num. unique all: 2082 / % possible all: 84.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→19.73 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.548 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23231 817 5 %RANDOM
Rwork0.19313 ---
all0.195 15492 --
obs0.19508 15492 93.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.002 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1547 0 10 126 1683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211584
X-RAY DIFFRACTIONr_bond_other_d0.0010.021476
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9732141
X-RAY DIFFRACTIONr_angle_other_deg0.71233424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.6645211
X-RAY DIFFRACTIONr_chiral_restr0.0940.2239
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021815
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02318
X-RAY DIFFRACTIONr_nbd_refined0.240.2354
X-RAY DIFFRACTIONr_nbd_other0.2790.21748
X-RAY DIFFRACTIONr_nbtor_other0.0880.21004
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.350.228
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3830.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.28
X-RAY DIFFRACTIONr_mcbond_it3.81321023
X-RAY DIFFRACTIONr_mcangle_it5.48331623
X-RAY DIFFRACTIONr_scbond_it5.4212561
X-RAY DIFFRACTIONr_scangle_it7.9993518
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.308 53
Rwork0.248 993
obs-993

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