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- PDB-1dbx: Crystal structure of cysteinyl-tRNA(Pro) deacylase from H. influe... -

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Basic information

Entry
Database: PDB / ID: 1dbx
TitleCrystal structure of cysteinyl-tRNA(Pro) deacylase from H. influenzae (HI1434)
Componentscysteinyl-tRNA(Pro) deacylase
KeywordsHYDROLASE / STRUCTURAL GENOMICS / YBAK / Structure 2 Function Project / S2F
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases / Ala-tRNA(Pro) deacylase activity / lyase activity / translation / cytoplasm
Similarity search - Function
Prolyl-tRNA editing protein, YbaK/EbsC / 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
Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase YbaK
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsZhang, H. / Huang, K. / Li, Z. / Herzberg, O. / Structure 2 Function Project (S2F)
CitationJournal: Proteins / Year: 2000
Title: Crystal structure of YbaK protein from Haemophilus influenzae (HI1434) at 1.8 A resolution: functional implications.
Authors: Zhang, H. / Huang, K. / Li, Z. / Banerjei, L. / Fisher, K.E. / Grishin, N.V. / Eisenstein, E. / Herzberg, O.
History
DepositionNov 3, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 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_conn / struct_ref_seq_dif
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
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 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: cysteinyl-tRNA(Pro) deacylase
B: cysteinyl-tRNA(Pro) deacylase


Theoretical massNumber of molelcules
Total (without water)34,5472
Polymers34,5472
Non-polymers00
Water6,738374
1
A: cysteinyl-tRNA(Pro) deacylase


Theoretical massNumber of molelcules
Total (without water)17,2741
Polymers17,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: cysteinyl-tRNA(Pro) deacylase


Theoretical massNumber of molelcules
Total (without water)17,2741
Polymers17,2741
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.560, 42.210, 54.160
Angle α, β, γ (deg.)109.07, 100.32, 90.62
Int Tables number1
Space group name H-MP1

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Components

#1: Protein cysteinyl-tRNA(Pro) deacylase / HI1434


Mass: 17273.607 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Description: IMPACT I SYSTEM FROM NEW ENGLAND BIOLABS / Gene: YbaK / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P45202
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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 Å3/Da / Density % sol: 28 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16 mg/mlprotein1drop
250 mMpotassium phosphate1drop
30.1 mMEDTA1drop
45 mMdithiothreitol1drop
5100 mMTris-HCl1reservoir
625-35 %mPEG50001reservoir
73 %propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95
DetectorType: BRANDEIS / Detector: CCD / Date: Oct 27, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 49134 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.033
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.129 / % possible all: 97.6
Reflection
*PLUS
Num. measured all: 96443
Reflection shell
*PLUS
% possible obs: 97.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: YBAK structure in C2 space group, 1dbu

1dbu


Resolution: 1.8→20 Å / Cross valid method: free-R / σ(F): 0 / σ(I): -3 / ESU R: 0.17 / ESU R Free: 0.172
RfactorNum. reflection% reflectionSelection details
Rfree0.259 2446 10 %RANDOM
Rwork0.183 ---
obs-24752 97.8 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2304 0 0 374 2678
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rfree: 0.27 / Rfactor Rwork: 0.176

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