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- PDB-1j5u: CRYSTAL STRUCTURE OF AN ARCHEASE, POSSIBLE CHAPERONE (TM1083) FRO... -

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Basic information

Entry
Database: PDB / ID: 1j5u
TitleCRYSTAL STRUCTURE OF AN ARCHEASE, POSSIBLE CHAPERONE (TM1083) FROM THERMOTOGA MARITIMA AT 2.0 A RESOLUTION
Componentsarchease, possible chaperone
KeywordsCHAPERONE / ARCHEASE / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI
Function / homology
Function and homology information


tRNA processing / metal ion binding
Similarity search - Function
Archease, Possible Chaperone; Chain: A; domain 1 / Archease domain / Archease / Archease domain / Archease domain superfamily / Archease protein family (MTH1598/TM1083) / 3-Layer(bab) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of archease, possible chaperone (TM1083) from Thermotoga maritima at 2.0 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 3, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 31, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN Calcium ion assigned based on electron density and coordination.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: archease, possible chaperone
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3302
Polymers16,2901
Non-polymers401
Water2,126118
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.28, 105.28, 105.28
Angle α, β, γ (deg.)90, 90, 90
Int Tables number212
Space group name H-MP4332

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Components

#1: Protein archease, possible chaperone


Mass: 16289.958 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1083 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0H1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.93 Å3/Da / Density % sol: 57.74 %
Crystal growTemperature: 293 K / pH: 4.6
Details: 0.14 M CaCl2; 14 % isoprop; 0.07 M Acetate pH 4.6, 30 % Glycerol, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K, pH 4.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.925223, 0.978645, 0.979029
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2002
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9252231
20.9786451
30.9790291
ReflectionResolution: 2→35.176 Å / Num. obs: 13851 / % possible obs: 99.3 % / Redundancy: 5.1 % / Biso Wilson estimate: 32.5 Å2 / Rsym value: 0.071 / Net I/σ(I): 16.8
Reflection shellResolution: 2→2.11 Å / Redundancy: 4 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.277 / % possible all: 98.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
CCP4data reduction
CCP4model building
SOLVEphasing
RESOLVEmodel building
CNS1refinement
CCP4(SCALA)data scaling
CCP4phasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→35.09 Å / Cross valid method: THROUGHOUT / σ(F): 2
Stereochemistry target values: STANDARD CNS DICTIONARY/ENGH AND HUBER
Details: SOME DENSITY PRESENT FOR THE FIRST 3 RESIDUES IN THE HISTIDINE TAG, BUT TOO WEAK TO INTERPRET. THE PACKING OF THE HISTIDINE TAG HAS DISRUPTED THE CONFORMATION OF THE FIRST 7 RESIDUES AT THE N TERMINUS.
RfactorNum. reflection% reflectionSelection details
Rfree0.271 674 4.8 %RANDOM
Rwork0.212 ---
obs0.212 13430 99 %-
all-13890 --
Solvent computationSolvent model: BULK SOLVENT CORRECTION / Bsol: 36.8 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error6 Å0.93 Å
Refinement stepCycle: LAST / Resolution: 2→35.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1065 0 1 118 1184
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.54
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4131.5
X-RAY DIFFRACTIONc_mcangle_it2.0052
X-RAY DIFFRACTIONc_scbond_it2.6822
X-RAY DIFFRACTIONc_scangle_it3.8272.5
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2482 40 4.1 %
Rwork0.2102 930 -

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