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

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Basic information

Entry
Database: PDB / ID: 1dbu
TitleCrystal structure of cysteinyl-tRNA(Pro) deacylase protein 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 / MAD / 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 1.3Nov 13, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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: cysteinyl-tRNA(Pro) deacylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4742
Polymers17,2741
Non-polymers2011
Water3,081171
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.570, 42.490, 32.540
Angle α, β, γ (deg.)90.00, 104.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 17273.607 Da / Num. of mol.: 1
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: Chemical ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 1.99 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: 1.0091
DetectorType: BRANDEIS / Detector: CCD / Date: Oct 27, 1998
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0091 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 25089 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.059
Reflection shellResolution: 1.8→1.86 Å / Rmerge(I) obs: 0.357 / % possible all: 98
Reflection
*PLUS
Num. measured all: 47185
Reflection shell
*PLUS
% possible obs: 98 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 1.8→20 Å / Cross valid method: free-R / σ(F): 0 / σ(I): 0 / ESU R: 0.173 / ESU R Free: 0.171
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1260 10 %RANDOM
Rwork0.193 ---
obs-12727 99.6 %-
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1187 0 1 171 1359
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
Software
*PLUS
Name: REFMAC / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rfree: 0.282 / Rfactor Rwork: 0.215

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