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- PDB-2zk7: Structure of a C-terminal deletion mutant of Thermoplasma acidoph... -

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Basic information

Entry
Database: PDB / ID: 2zk7
TitleStructure of a C-terminal deletion mutant of Thermoplasma acidophilum aldohexose dehydrogenase (AldT)
ComponentsGlucose 1-dehydrogenase related protein
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
: / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Glucose 1-dehydrogenase related protein
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsNishioka, T. / Yasutake, Y. / Nishiya, Y. / Tamura, N. / Tamura, T.
CitationJournal: Proteins / Year: 2009
Title: C-terminal tail derived from the neighboring subunit is critical for the activity of Thermoplasma acidophilum D-aldohexose dehydrogenase
Authors: Nishioka, T. / Yasutake, Y. / Nishiya, Y. / Tamura, N. / Tamura, T.
History
DepositionMar 12, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 13, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose 1-dehydrogenase related protein
B: Glucose 1-dehydrogenase related protein


Theoretical massNumber of molelcules
Total (without water)56,5972
Polymers56,5972
Non-polymers00
Water66737
1
A: Glucose 1-dehydrogenase related protein
B: Glucose 1-dehydrogenase related protein

A: Glucose 1-dehydrogenase related protein
B: Glucose 1-dehydrogenase related protein


Theoretical massNumber of molelcules
Total (without water)113,1944
Polymers113,1944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_455-x+y-1,y,-z+1/21
Buried area10330 Å2
ΔGint-90.2 kcal/mol
Surface area36380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.238, 68.238, 337.356
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Glucose 1-dehydrogenase related protein / AldT / aldohexose dehydrogenase


Mass: 28298.395 Da / Num. of mol.: 2
Mutation: C-terminal deletion (residues 250-255 are deleted)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: Ta0754 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIL / References: UniProt: Q9HK51, EC: 1.1.1.118
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsSIX C-TERMINAL RESIDUES(250-255) ARE DELETED.

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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 Å3/Da / Density % sol: 38.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M imidazol, 0.8M Na/K tartrate, 0.1M NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 21, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 13725 / Num. obs: 13725 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 18.5 % / Biso Wilson estimate: 74.2 Å2 / Rsym value: 0.106 / Net I/σ(I): 43.5
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 18.4 % / Mean I/σ(I) obs: 7.9 / Num. unique all: 1308 / Rsym value: 0.611 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DTD

2dtd


Resolution: 2.71→40.72 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.905 / SU B: 37.95 / SU ML: 0.363 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.426 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28911 662 4.9 %RANDOM
Rwork0.23738 ---
obs0.23979 12962 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.567 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20.26 Å20 Å2
2--0.53 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 2.71→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3661 0 0 37 3698
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223732
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.9595052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6635472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.5223.529153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.57115643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9381525
X-RAY DIFFRACTIONr_chiral_restr0.0810.2577
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022771
X-RAY DIFFRACTIONr_nbd_refined0.2030.21788
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22587
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2122
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.2123
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.27
X-RAY DIFFRACTIONr_mcbond_it0.3651.52425
X-RAY DIFFRACTIONr_mcangle_it0.64623822
X-RAY DIFFRACTIONr_scbond_it0.69631469
X-RAY DIFFRACTIONr_scangle_it1.1374.51230
LS refinement shellResolution: 2.707→2.777 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.354 39 -
Rwork0.283 921 -
obs-960 99.79 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.46480.189-0.10132.81850.94817.51890.1242-0.00810.0996-0.10260.2654-0.5219-1.00821.3671-0.3896-0.1843-0.1980.0627-0.1312-0.0782-0.0753-21.771610.238693.1617
23.76081.1368-0.55411.6908-1.10994.4495-0.2564-0.6896-0.16650.34910.1171-0.17980.81630.47740.13930.04630.2559-0.026-0.2260.0416-0.135-27.0154-20.857898.5854
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 8110 - 89
2X-RAY DIFFRACTION1AA93 - 131101 - 139
3X-RAY DIFFRACTION1AA140 - 247148 - 255
4X-RAY DIFFRACTION2BB2 - 24710 - 255

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