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- PDB-1s12: Crystal structure of TM1457 -

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Basic information

Entry
Database: PDB / ID: 1s12
TitleCrystal structure of TM1457
Componentshypothetical protein TM1457
Keywordsstructural genomics / unknown function / crystal / hypothetical protein / PSI / Berkeley Structural Genomics Center / BSGC / Protein Structure Initiative
Function / homology
Function and homology information


cysteine-type peptidase activity / ribosome biogenesis / proteolysis
Similarity search - Function
Cysteine protease Prp / Cysteine protease Prp / Cysteine protease Prp superfamily / Cysteine protease Prp / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Ribosomal processing cysteine protease Prp
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsShin, D.H. / Lou, Y. / Jancarik, J. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.Struct.Biol. / Year: 2005
Title: Crystal structure of TM1457 from Thermotoga maritima.
Authors: Shin, D.H. / Lou, Y. / Jancarik, J. / Yokota, H. / Kim, R. / Kim, S.H.
History
DepositionJan 5, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_related / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_related.db_name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein TM1457
B: hypothetical protein TM1457
C: hypothetical protein TM1457
D: hypothetical protein TM1457
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4668
Polymers42,2294
Non-polymers2364
Water6,648369
1
A: hypothetical protein TM1457
D: hypothetical protein TM1457
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2334
Polymers21,1152
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-19 kcal/mol
Surface area9620 Å2
MethodPISA
2
B: hypothetical protein TM1457
C: hypothetical protein TM1457
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,2334
Polymers21,1152
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-19 kcal/mol
Surface area9580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.890, 63.280, 65.500
Angle α, β, γ (deg.)90.00, 108.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
hypothetical protein TM1457


Mass: 10557.347 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1G8
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4M NaCitrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2002 / Details: Monochromator
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→48.4 Å / Num. all: 26957 / Num. obs: 26634 / % possible obs: 98.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 9 Å2
Reflection shellResolution: 2→2.03 Å / % possible all: 94.6

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.98 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 167885.36 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2225 10 %RANDOM
Rwork0.214 ---
all0.22 ---
obs0.214 22168 82.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.3717 Å2 / ksol: 0.320048 e/Å3
Displacement parametersBiso mean: 35.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.88 Å20 Å26.36 Å2
2---7.08 Å20 Å2
3---11.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 16 369 3303
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it3.611.5
X-RAY DIFFRACTIONc_mcangle_it5.712
X-RAY DIFFRACTIONc_scbond_it7.132
X-RAY DIFFRACTIONc_scangle_it11.392.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.261 269 10.4 %
Rwork0.238 2315 -
obs--57.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ACT.PARAM

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