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- PDB-1bsj: COBALT DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI -

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Basic information

Entry
Database: PDB / ID: 1bsj
TitleCOBALT DEFORMYLASE INHIBITOR COMPLEX FROM E.COLI
ComponentsPROTEIN (PEPTIDE DEFORMYLASE)
KeywordsHYDROLASE / DEFORMYLASE / INHIBITOR / METALLOPROTEINASE
Function / homology
Function and homology information


peptide deformylase / peptide deformylase activity / : / ferrous iron binding / ribosome binding / hydrolase activity / translation / zinc ion binding / cytosol
Similarity search - Function
Peptide Deformylase / Peptide deformylase / Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Chem-MLN / PHOSPHATE ION / Peptide deformylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHao, B. / Gong, W. / Rajagopalan, P.T. / Hu, Y. / Pei, D. / Chan, M.K.
Citation
Journal: Biochemistry / Year: 1999
Title: Structural basis for the design of antibiotics targeting peptide deformylase.
Authors: Hao, B. / Gong, W. / Rajagopalan, P.T. / Zhou, Y. / Pei, D. / Chan, M.K.
#1: Journal: Biochemistry / Year: 1997
Title: Crystal Structure of the Escherichia Coli Peptide Deformylase
Authors: Chan, M.K. / Gong, W. / Rajagopalan, P.T. / Hao, B. / Tsai, C. / Pei, D.
History
DepositionAug 28, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Apr 15, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN (PEPTIDE DEFORMYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8264
Polymers19,2261
Non-polymers5993
Water21612
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.080, 99.080, 111.040
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein PROTEIN (PEPTIDE DEFORMYLASE) / 3.5.1.27


Mass: 19226.248 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cell line: BL21(DE3) / References: UniProt: P0A6K3, EC: 3.5.1.27
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-MLN / (S)-2-(PHOSPHONOXY)CAPROYL-L-LEUCYL-P-NITROANILIDE


Mass: 445.404 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H28N3O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 4.1 Å3/Da / Density % sol: 65 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.1 MTris-HCl1reservoir
21.9 M1reservoirNH4H2PO4
314.4 mg/mlprotein1drop
420 mMsodium phosphate1drop
510 mM1dropNaCl
60.86 Mammonium sulfate1drop
71 mMinhibitor1drop

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: May 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 6591 / % possible obs: 96.3 % / Observed criterion σ(I): 0 / Redundancy: 8.1 % / Rmerge(I) obs: 0.085 / Rsym value: 8.5
Reflection shellResolution: 3→3.1 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.246 / Rsym value: 24.6 / % possible all: 97.3
Reflection
*PLUS
Highest resolution: 2.1 Å / Num. obs: 16692 / % possible obs: 87.3 % / Num. measured all: 118933 / Rmerge(I) obs: 0.074
Reflection shell
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 2.19 Å / % possible obs: 87.7 % / Rmerge(I) obs: 0.236

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DFF

1dff


Resolution: 3→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.207 501 7.3 %RANDOM
Rwork0.168 ---
obs0.168 6591 96.3 %-
Refinement stepCycle: LAST / Resolution: 3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1329 0 35 12 1376
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.594
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 3→3.14 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.262 60 7.3 %
Rwork0.212 666 -
obs--89.2 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 20 Å / Num. reflection obs: 16692 / σ(F): 0 / % reflection Rfree: 8 % / Rfactor obs: 0.199 / Rfactor Rfree: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 3 Å / Rfactor Rfree: 0.262 / % reflection Rfree: 7.3 % / Rfactor Rwork: 0.212

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