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- PDB-1lxn: X-RAY STRUCTURE OF MTH1187 NORTHEAST STRUCTURAL GENOMICS CONSORTI... -

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Basic information

Entry
Database: PDB / ID: 1lxn
TitleX-RAY STRUCTURE OF MTH1187 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET TT272
ComponentsHYPOTHETICAL PROTEIN MTH1187
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HYPOTHETICAL STRUCTURE / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


Thiamine-binding protein / : / Thiamine-binding protein / Alpha-Beta Plaits - #930 / MTH1187/YkoF-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
UPF0045 protein MTH_1187
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsTao, X. / Khayat, R. / Christendat, D. / Savchenko, A. / Xu, X. / Edwards, A. / Arrowsmith, C.H. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: Proteins / Year: 2003
Title: Crystal Structures of MTH1187 and its Yeast Ortholog YBL001C
Authors: Tao, X. / Khayat, R. / Christendat, D. / Savchenko, A. / Xu, X. / Goldsmith-Fischman, S. / Honig, B. / Edwards, A. / Arrowsmith, C.H. / Tong, L.
History
DepositionJun 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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: HYPOTHETICAL PROTEIN MTH1187
B: HYPOTHETICAL PROTEIN MTH1187
C: HYPOTHETICAL PROTEIN MTH1187
D: HYPOTHETICAL PROTEIN MTH1187
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,38810
Polymers43,8124
Non-polymers5766
Water2,504139
1
A: HYPOTHETICAL PROTEIN MTH1187
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0492
Polymers10,9531
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HYPOTHETICAL PROTEIN MTH1187
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,0492
Polymers10,9531
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: HYPOTHETICAL PROTEIN MTH1187
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1453
Polymers10,9531
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: HYPOTHETICAL PROTEIN MTH1187
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1453
Polymers10,9531
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13280 Å2
ΔGint-182 kcal/mol
Surface area14930 Å2
MethodPISA, PQS
6
A: HYPOTHETICAL PROTEIN MTH1187
D: HYPOTHETICAL PROTEIN MTH1187
hetero molecules

B: HYPOTHETICAL PROTEIN MTH1187
C: HYPOTHETICAL PROTEIN MTH1187
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,38810
Polymers43,8124
Non-polymers5766
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation17_455x-1/4,z+1/4,-y+1/41
Buried area4130 Å2
ΔGint-97 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.365, 175.365, 175.365
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132

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Components

#1: Protein
HYPOTHETICAL PROTEIN MTH1187


Mass: 10953.027 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Production host: Escherichia coli (E. coli) / References: UniProt: O27255
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mMHEPES1drop
2500 mM1dropNaCl
320 mg/mlprotein1drop
40.1 Msodium acetate1reservoirpH4.6
52 Mammonium sulfate1reservoir
614 %glycerol1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X4A10.9791
SYNCHROTRONAPS 19-BM20.97799
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 27, 2002
CUSTOM-MADE2CCDMar 26, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111 CHANNELMADMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.977991
ReflectionResolution: 2.3→20 Å / Num. all: 40380 / Num. obs: 40380 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19.6 Å2
Reflection shellResolution: 2.3→2.38 Å / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.3 Å / Num. measured all: 425012 / Rmerge(I) obs: 0.058

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1.1refinement
RefinementMethod to determine structure: MIR / Resolution: 2.3→19.99 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2127257.29 / Data cutoff high rms absF: 2127257.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.245 2968 7.7 %RANDOM
Rwork0.216 ---
all-40380 --
obs-38721 93.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.8139 Å2 / ksol: 0.394027 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.61 Å20 Å20 Å2
2---0.81 Å20 Å2
3----0.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 30 139 3182
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.7
X-RAY DIFFRACTIONc_improper_angle_d0.63
X-RAY DIFFRACTIONc_mcbond_it1.361.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it3.132
X-RAY DIFFRACTIONc_scangle_it4.392.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.259 433 7.6 %
Rwork0.217 5278 -
obs--84.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMTOP.SO4
X-RAY DIFFRACTION3PARAM.SO4
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 20 Å / Num. reflection obs: 77165
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.63

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