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- PDB-2yw3: Crystal Structure Analysis of the 4-hydroxy-2-oxoglutarate aldola... -

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Basic information

Entry
Database: PDB / ID: 2yw3
TitleCrystal Structure Analysis of the 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase from TTHB1
Components4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase
KeywordsLYASE / aldolase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


2-dehydro-3-deoxy-phosphogluconate aldolase / 2-dehydro-3-deoxy-phosphogluconate aldolase activity
Similarity search - Function
KDPG/KHG aldolase, active site 1 / KDPG and KHG aldolases active site. / KDPG/KHG aldolase / KDPG and KHG aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 2-dehydro-3-deoxy-phosphogluconate aldolase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsKawano, Y. / Hashimoto, K. / Kamiya, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be published
Title: Crystal Structure Analysis of the 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase from TTHB1
Authors: Kawano, Y. / Hashimoto, K. / Kamiya, N.
History
DepositionApr 19, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase
B: 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase
C: 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase
D: 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase
E: 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase
F: 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,08623
Polymers130,4726
Non-polymers1,61517
Water18,4291023
1
A: 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase
B: 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase
C: 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7118
Polymers65,2363
Non-polymers4755
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-52 kcal/mol
Surface area22400 Å2
MethodPISA, PQS
2
D: 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase
E: 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase
F: 4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,37615
Polymers65,2363
Non-polymers1,14012
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7210 Å2
ΔGint-110 kcal/mol
Surface area22730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.922, 72.685, 161.312
Angle α, β, γ (deg.)90.00, 91.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
4-hydroxy-2-oxoglutarate aldolase/2-deydro-3-deoxyphosphogluconate aldolase


Mass: 21745.330 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Production host: Escherichia coli (E. coli)
References: UniProt: Q53W90, 2-dehydro-3-deoxy-phosphogluconate aldolase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1023 / 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: 2.83 Å3/Da / Density % sol: 56.48 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: 0.4M Potassium sodium tartrate tetrahydrate, pH 4.1, VAPOR DIFFUSION, HANGING DROP, temperature 301K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 0.97937 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 12, 2005
RadiationMonochromator: Diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 1.67→35.6 Å / Num. all: 145847 / Num. obs: 145847 / % possible obs: 86.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 11.39
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.303 / Mean I/σ(I) obs: 3.52 / Num. unique all: 11116 / % possible all: 65.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
RapidAutodata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MXS

1mxs


Resolution: 1.67→35.58 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.938 / SU B: 1.727 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.214 14564 10 %RANDOM
Rwork0.182 ---
all0.185 131262 --
obs0.185 131262 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.695 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20.01 Å2
2--0.36 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.67→35.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8808 0 84 1023 9915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0229223
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5332.03612585
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.35251239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.04522.661327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59151562
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5331584
X-RAY DIFFRACTIONr_chiral_restr0.0950.21506
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026776
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.24910
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.26290
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2899
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.2115
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2120.237
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0341.56074
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.67929494
X-RAY DIFFRACTIONr_scbond_it2.69533386
X-RAY DIFFRACTIONr_scangle_it4.5494.53061
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.669→1.712 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 756 -
Rwork0.229 7114 -
obs--100 %

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