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- PDB-2z0x: Crystal structure of ProX-CysSA complex from T. thermophilus -

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Basic information

Entry
Database: PDB / ID: 2z0x
TitleCrystal structure of ProX-CysSA complex from T. thermophilus
ComponentsPutative uncharacterized protein TTHA1699
KeywordsTRANSLATION / Protein-CysSA complex / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


aminoacyl-tRNA deacylase activity
Similarity search - Function
YbaK protein / YbaK/aminoacyl-tRNA synthetase-associated domain / YbaK/aminoacyl-tRNA synthetase-associated domain / Aminoacyl-tRNA editing domain / YbaK/aminoacyl-tRNA synthetase-associated domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
5'-O-(N-(L-CYSTEINYL)-SULFAMOYL)ADENOSINE / YbaK/aminoacyl-tRNA synthetase-associated domain-containing protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Terada, T. / Kuramitsu, S. / Shirouzu, M. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of ProX-CysSA complex from T. thermophilus
Authors: Murayama, K. / Kato-Murayama, M. / Terada, T. / Shirouzu, M. / Yokoyama, S.
History
DepositionMay 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Putative uncharacterized protein TTHA1699
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,0242
Polymers16,5751
Non-polymers4491
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.512, 50.613, 81.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein TTHA1699


Mass: 16575.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHN1
#2: Chemical ChemComp-5CA / 5'-O-(N-(L-CYSTEINYL)-SULFAMOYL)ADENOSINE


Mass: 449.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H19N7O7S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / 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: 1.97 Å3/Da / Density % sol: 37.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG 3350, 0.1M Hepes, 30mM CysSA, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jul 28, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. obs: 16242 / % possible obs: 96.9 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 16 Å2 / Rsym value: 0.022 / Net I/σ(I): 59
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 11.6 / Rsym value: 0.079 / % possible all: 77.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CX5

2cx5


Resolution: 1.64→26.75 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1095505.74 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.186 788 4.9 %RANDOM
Rwork0.158 ---
obs-16172 97 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 25.1754 Å2 / ksol: 0.286568 e/Å3
Displacement parametersBiso mean: 14.4 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.04 Å
Refinement stepCycle: LAST / Resolution: 1.64→26.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1161 0 29 255 1445
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d1.39
X-RAY DIFFRACTIONc_mcbond_it1.791.5
X-RAY DIFFRACTIONc_mcangle_it2.412
X-RAY DIFFRACTIONc_scbond_it3.372
X-RAY DIFFRACTIONc_scangle_it4.622.5
LS refinement shellResolution: 1.64→1.74 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 111 4.9 %
Rwork0.224 2150 -
obs--82.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cyssa.param
X-RAY DIFFRACTION3water_rep.param

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