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- PDB-3lnw: Close correlation of protein thermostability and self-buried area... -

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Basic information

Entry
Database: PDB / ID: 3lnw
TitleClose correlation of protein thermostability and self-buried area rate revealed by crystal structure of HPr from Thermoanaerobacter tengcongensis MB4
ComponentsPhosphotransferase system, HPr-related proteins
KeywordsTRANSFERASE / HPr / thermostability mechanism / self-buried area / hydrophobic effect / Thermoanaerobacter tengcongensis / Kinase / Phosphotransferase system
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / cytoplasm
Similarity search - Function
Phosphotransferase system, HPr histidine phosphorylation site / PTS HPR domain histidine phosphorylation site signature. / HPr-like / Phosphocarrier protein HPr-like / HPr-like superfamily / : / PTS HPr component phosphorylation site / PTS HPR domain profile. / Histidine-containing Protein; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphocarrier protein HPr
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsGao, G.G. / Feng, C. / Gao, F. / Liu, Y.
CitationJournal: To be Published
Title: Close correlation of protein thermostability and self-buried area rate revealed by crystal structure of HPr from Thermoanaerobacter tengcongensis MB4
Authors: Gao, G.G. / Feng, C. / Gao, F. / Liu, Y.
History
DepositionFeb 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphotransferase system, HPr-related proteins
B: Phosphotransferase system, HPr-related proteins
C: Phosphotransferase system, HPr-related proteins


Theoretical massNumber of molelcules
Total (without water)28,8603
Polymers28,8603
Non-polymers00
Water2,432135
1
A: Phosphotransferase system, HPr-related proteins


Theoretical massNumber of molelcules
Total (without water)9,6201
Polymers9,6201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphotransferase system, HPr-related proteins


Theoretical massNumber of molelcules
Total (without water)9,6201
Polymers9,6201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Phosphotransferase system, HPr-related proteins


Theoretical massNumber of molelcules
Total (without water)9,6201
Polymers9,6201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.972, 67.972, 50.444
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: GLY / End label comp-ID: GLY / Auth seq-ID: 1 - 86 / Label seq-ID: 1 - 86

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 1:86 )AA
2chain B and (resseq 1:86 )BB
3chain C and (resseq 1:86 )CC

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Components

#1: Protein Phosphotransferase system, HPr-related proteins


Mass: 9620.015 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: MB4 / Gene: FruB, TTE1820 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8R910
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 24

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 15% PEG 20000, 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.485
ReflectionResolution: 2.3→50 Å / Num. obs: 11556 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 24.271
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.245 / Mean I/σ(I) obs: 8.404 / Num. unique all: 63655 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.5_2)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.302→38.304 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0.16 / Phase error: 24.46 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2206 -4.79 %
Rwork0.1899 --
obs0.1919 11474 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.915 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 86.8 Å2 / Biso mean: 31.204 Å2 / Biso min: 12.13 Å2
Baniso -1Baniso -2Baniso -3
1-4.451 Å2-0 Å2-0 Å2
2--4.451 Å20 Å2
3----8.902 Å2
Refinement stepCycle: LAST / Resolution: 2.302→38.304 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 0 135 2097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012031
X-RAY DIFFRACTIONf_angle_d1.3762712
X-RAY DIFFRACTIONf_dihedral_angle_d16.77771
X-RAY DIFFRACTIONf_chiral_restr0.134318
X-RAY DIFFRACTIONf_plane_restr0.004342
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A654X-RAY DIFFRACTIONPOSITIONAL0.043
12B654X-RAY DIFFRACTIONPOSITIONAL0.043
13C654X-RAY DIFFRACTIONPOSITIONAL0.034
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.303-2.5350.2581310.2392705283694
2.535-2.9010.2241290.2142738286795
2.901-3.650.2121520.1792711286394
3.65-19.1530.2151360.1732735287195
Refinement TLS params.Method: refined / Origin x: -10.9682 Å / Origin y: -19.0853 Å / Origin z: 10.7994 Å
111213212223313233
T0.0911 Å2-0.013 Å2-0.0056 Å2-0.0817 Å2-0.005 Å2--0.0686 Å2
L0.2266 °2-0.0748 °2-0.051 °2-0.1312 °2-0.0964 °2--0.1269 °2
S-0.0002 Å °0.0213 Å °0.0157 Å °-0.0122 Å °-0.0061 Å °-0.0069 Å °0.0135 Å °0.0067 Å °0.0048 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 86
2X-RAY DIFFRACTION1allB1 - 86
3X-RAY DIFFRACTION1allC1 - 86
4X-RAY DIFFRACTION1allB - A1 - 135

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