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- PDB-3cq3: Structure of the DTDP-4-Keto-L-Rhamnose Reductase related protein... -

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Basic information

Entry
Database: PDB / ID: 3cq3
TitleStructure of the DTDP-4-Keto-L-Rhamnose Reductase related protein (other form) from Thermus Thermophilus HB8
ComponentsPutative uncharacterized protein TTHB138
KeywordsOXIDOREDUCTASE / Thermus Thermophilus / DTDP-4-Keto-L-Rhamnose Reductase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyFe-S cluster assembly (FSCA) / MIP18 family-like / Iron-sulfur cluster assembly protein / Fe-S cluster assembly domain superfamily / GMP Synthetase; Chain A, domain 3 / 2-Layer Sandwich / Alpha Beta / MIP18 family-like domain-containing protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJeyakanthan, J. / Kanaujia, S.P. / Sekar, K. / Satoh, S. / Kitamura, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure of the DTDP-4-Keto-L-Rhamnose Reductase related protein (other form) from Thermus Thermophilus HB8
Authors: Jeyakanthan, J. / Kanaujia, S.P. / Sekar, K. / Satoh, S. / Kitamura, Y. / Yokoyama, S. / Kurmamitsu, S.
History
DepositionApr 2, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 7, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 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
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein TTHB138
B: Putative uncharacterized protein TTHB138
C: Putative uncharacterized protein TTHB138
D: Putative uncharacterized protein TTHB138
E: Putative uncharacterized protein TTHB138
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,08623
Polymers57,4755
Non-polymers1,61118
Water6,990388
1
A: Putative uncharacterized protein TTHB138
hetero molecules

A: Putative uncharacterized protein TTHB138
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,97210
Polymers22,9902
Non-polymers9828
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
Buried area2300 Å2
ΔGint-30.7 kcal/mol
Surface area11790 Å2
MethodPISA
2
B: Putative uncharacterized protein TTHB138
C: Putative uncharacterized protein TTHB138
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,59110
Polymers22,9902
Non-polymers6018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-27.6 kcal/mol
Surface area10640 Å2
MethodPISA
3
D: Putative uncharacterized protein TTHB138
E: Putative uncharacterized protein TTHB138
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5098
Polymers22,9902
Non-polymers5196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1940 Å2
ΔGint-24.4 kcal/mol
Surface area11140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.122, 175.122, 99.095
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Putative uncharacterized protein TTHB138 / DTDP-4-Keto-L-Rhamnose Reductase


Mass: 11495.020 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q53W28

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Non-polymers , 5 types, 406 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 / Polyethylene glycol


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 3.3 Å3/Da / Density % sol: 62.78 % / Description: The file contains friedel pairs
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 18% PEG400, 0.1M Na Acetate, 0.1M Magnesium Chloride , pH4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 14, 2004 / Details: RH Coated Bent-Cyrindrical MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 82251 / % possible obs: 99.8 % / Biso Wilson estimate: 23.8 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.089
Reflection shellResolution: 2.1→2.18 Å / Rmerge(I) obs: 0.28 / Rsym value: 0.089 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CU6

2cu6


Resolution: 2.1→43.61 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 694419.47 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: The file contains friedel pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.22 4000 4.9 %RANDOM
Rwork0.196 ---
obs0.196 82194 95.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.6255 Å2 / ksol: 0.372384 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.73 Å20 Å20 Å2
2---4.73 Å20 Å2
3---9.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→43.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3850 0 103 388 4341
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_improper_angle_d0.92
LS refinement shellResolution: 2.1→2.2 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.282 424 4.5 %
Rwork0.25 9034 -
obs--88.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ligand.paramligand.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION5water_rep.paramwater_protin.top

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