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- PDB-2cbn: Crystal structure of ZipD from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2cbn
TitleCrystal structure of ZipD from Escherichia coli
ComponentsRIBONUCLEASE Z
KeywordsHYDROLASE / PHOSPHODIESTERASE BETA LACTAMASE TRNASE Z / METAL- BINDING / ENDONUCLEASE / TRNA PROCESSING / ZINC
Function / homology
Function and homology information


: / 3'-tRNA processing endoribonuclease activity / RNA exonuclease activity, producing 5'-phosphomonoesters / RNA endonuclease activity, producing 5'-phosphomonoesters / RNA exonuclease activity / nuclease activity / tRNA processing / Hydrolases; Acting on ester bonds / zinc ion binding / metal ion binding
Similarity search - Function
Ribonuclease BN / Ribonuclease Z/BN / Beta-lactamase superfamily domain / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Metallo-beta-lactamase; Chain A / Metallo-beta-lactamase superfamily / Metallo-beta-lactamase / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsPohl, E. / Meyer-Klaucke, W. / Kostelecky, B.
CitationJournal: J.Bacteriol. / Year: 2006
Title: The Crystal Structure of the Zinc Phosphodiesterase from Escherichia Coli Provides Insight Into Function and Cooperativity of Trnase Z-Family Proteins.
Authors: Kostelecky, B. / Pohl, E. / Vogel, A. / Schilling, O. / Meyer-Klaucke, W.
History
DepositionJan 6, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Derived calculations / Refinement description / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0963
Polymers32,9661
Non-polymers1312
Water00
1
A: RIBONUCLEASE Z
hetero molecules

A: RIBONUCLEASE Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1936
Polymers65,9312
Non-polymers2624
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z1
Buried area3140 Å2
ΔGint-179.1 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.200, 147.200, 138.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein RIBONUCLEASE Z / ZINC PHOSPHODIESTERASE / RNASE Z / TRNASE Z / TRNA 3 / ENDONUCLEASE


Mass: 32965.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0A8V0, tRNase Z
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 6.8 Å3/Da / Density % sol: 81.78 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.24
DetectorType: MARRESEARCH / Detector: CCD / Details: MIRROR
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.24 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 20073 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 15 % / Biso Wilson estimate: 46.96 Å2 / Rmerge(I) obs: 0.07

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Processing

Software
NameVersionClassification
CNS1refinement
XDSdata reduction
XDSdata scaling
XPREPphasing
SHELXDphasing
SHELXEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.9→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.25 974 4.8 %RANDOM
Rwork0.23 ---
obs0.23 19099 99.7 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.17 Å2-12.102 Å20 Å2
2---8.17 Å20 Å2
3---16.34 Å2
Refinement stepCycle: LAST / Resolution: 2.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2267 0 2 0 2269
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
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_deg1.6
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_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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