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- PDB-2r91: Crystal Structure of KD(P)GA from T.tenax -

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Basic information

Entry
Database: PDB / ID: 2r91
TitleCrystal Structure of KD(P)GA from T.tenax
Components2-Keto-3-deoxy-(6-phospho-)gluconate aldolase
KeywordsLYASE / TIM barrel / aldolase / thermophilic
Function / homology
Function and homology information


2-dehydro-3-deoxy-D-gluconate aldolase / 2-dehydro-3-deoxy-D-gluconate aldolase activity / 2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity / (R,S)-4-hydroxy-2-oxoglutarate aldolase activity / 4-hydroxy-tetrahydrodipicolinate synthase activity / glyoxylate catabolic process / cytosol
Similarity search - Function
DapA-like / Dihydrodipicolinate synthetase family / Dihydrodipicolinate synthetase family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
2-dehydro-3-deoxy-D-gluconate/2-dehydro-3-deoxy-phosphogluconate aldolase
Similarity search - Component
Biological speciesThermoproteus tenax (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsPauluhn, A. / Pohl, E. / Lorentzen, E. / Siebers, B. / Ahmed, H. / Buchinger, S. / Schomburg, D.
CitationJournal: Proteins / Year: 2008
Title: Crystal structure and stereochemical studies of KD(P)G aldolase from Thermoproteus tenax.
Authors: Pauluhn, A. / Ahmed, H. / Lorentzen, E. / Buchinger, S. / Schomburg, D. / Siebers, B. / Pohl, E.
History
DepositionSep 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-Keto-3-deoxy-(6-phospho-)gluconate aldolase
D: 2-Keto-3-deoxy-(6-phospho-)gluconate aldolase
B: 2-Keto-3-deoxy-(6-phospho-)gluconate aldolase
C: 2-Keto-3-deoxy-(6-phospho-)gluconate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,4548
Polymers124,0694
Non-polymers3844
Water12,430690
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11860 Å2
ΔGint-135.2 kcal/mol
Surface area38470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.347, 150.347, 175.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: MET / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 21 - 306 / Label seq-ID: 1 - 286

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BC
3CD
4DB

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Components

#1: Protein
2-Keto-3-deoxy-(6-phospho-)gluconate aldolase


Mass: 31017.344 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoproteus tenax (archaea) / Gene: kdgA / Plasmid: pET-15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q704D1, Lyases; Carbon-carbon lyases; Aldehyde-lyases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 690 / 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: 3.99 Å3/Da / Density % sol: 69.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: HEPES/KOH, pH 7.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.905 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.905 Å / Relative weight: 1
ReflectionResolution: 2→48.17 Å / Num. all: 135342 / Num. obs: 135046 / Observed criterion σ(I): 3 / Redundancy: 9.9 % / Rmerge(I) obs: 0.065 / Rsym value: 0.087
Reflection shellResolution: 2→2.1 Å / Redundancy: 10 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 5.92 / Num. unique all: 18158 / Rsym value: 0.392 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
MAR345data collection
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementResolution: 2→48.17 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.644 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 6753 5 %RANDOM
Rwork0.184 ---
obs0.186 135044 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.08 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2---0.26 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 2→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8740 0 20 690 9450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0228928
X-RAY DIFFRACTIONr_angle_refined_deg1.4721.97712136
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.10751140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.23522.784388
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.875151420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5561584
X-RAY DIFFRACTIONr_chiral_restr0.1010.21380
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026812
X-RAY DIFFRACTIONr_nbd_refined0.2230.34315
X-RAY DIFFRACTIONr_nbtor_refined0.3150.56233
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.51088
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3330.368
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.8310.548
X-RAY DIFFRACTIONr_mcbond_it1.4325865
X-RAY DIFFRACTIONr_mcangle_it2.1239096
X-RAY DIFFRACTIONr_scbond_it1.71623477
X-RAY DIFFRACTIONr_scangle_it2.67233040
Refine LS restraints NCS

Ens-ID: 1 / Number: 2185 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1AMEDIUM POSITIONAL0.440.5
2BMEDIUM POSITIONAL0.460.5
3CMEDIUM POSITIONAL0.520.5
4DMEDIUM POSITIONAL0.470.5
1AMEDIUM THERMAL1.722
2BMEDIUM THERMAL2.362
3CMEDIUM THERMAL2.042
4DMEDIUM THERMAL1.682
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 492 -
Rwork0.22 9345 -
all-9837 -
obs--100 %

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