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- PDB-1bs6: PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM IN COMPLEX WITH TRIPE... -

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Basic information

Entry
Database: PDB / ID: 1bs6
TitlePEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER
Components
  • PROTEIN (MET-ALA-SER)
  • PROTEIN (PEPTIDE DEFORMYLASE)
KeywordsHYDROLASE / IRON METALLOPROTEASE / PROTEIN SYNTHESIS
Function / homology
Function and homology information


peptide deformylase / peptide deformylase activity / co-translational protein modification / 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
NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBecker, A. / Schlichting, I. / Kabsch, W. / Groche, D. / Schultz, S. / Wagner, A.F.V.
Citation
Journal: Nat.Struct.Biol. / Year: 1998
Title: Iron center, substrate recognition and mechanism of peptide deformylase.
Authors: Becker, A. / Schlichting, I. / Kabsch, W. / Groche, D. / Schultz, S. / Wagner, A.F.
#1: Journal: J.Biol.Chem. / Year: 1998
Title: Structure of Peptide Deformylase and Identification of the Substrate Binding Site
Authors: Becker, A. / Schlichting, I. / Kabsch, W. / Schultz, S. / Wagner, A.F.V.
#2: Journal: Biochem.Biophys.Res.Commun. / Year: 1998
Title: Isolation and Crystallization of Functionally Competent Escherichia Coli Peptide Deformylase Forms Containing Either Iron or Nickel in the Active Site
Authors: Groche, D. / Becker, A. / Schlichting, I. / Kabsch, W. / Schultz, S. / Wagner, A.F.V.
History
DepositionSep 1, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Aug 27, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: 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 / 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_asym_id / _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_asym_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.ptnr1_auth_asym_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_asym_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

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (PEPTIDE DEFORMYLASE)
B: PROTEIN (PEPTIDE DEFORMYLASE)
C: PROTEIN (PEPTIDE DEFORMYLASE)
D: PROTEIN (MET-ALA-SER)
E: PROTEIN (MET-ALA-SER)
F: PROTEIN (MET-ALA-SER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,96911
Polymers58,6016
Non-polymers3685
Water2,972165
1
A: PROTEIN (PEPTIDE DEFORMYLASE)
D: PROTEIN (MET-ALA-SER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5923
Polymers19,5342
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (PEPTIDE DEFORMYLASE)
E: PROTEIN (MET-ALA-SER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6884
Polymers19,5342
Non-polymers1552
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (PEPTIDE DEFORMYLASE)
F: PROTEIN (MET-ALA-SER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6884
Polymers19,5342
Non-polymers1552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.800, 64.100, 85.100
Angle α, β, γ (deg.)90.00, 123.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (PEPTIDE DEFORMYLASE) / E.C.3.5.1.31 HYDROLASE / PDF


Mass: 19226.248 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: PDF PROTEIN FORM ESCHERICHIA COLI IS CRYSTALLIZED AS NI2+ CONTAINING FORM, COCRYSTALLIZED WITH PRODUCT PEPTIDE MET-ALA-SER (MAS)
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: JM109 / Cellular location: CYTOPLASMA / Gene: DEF / Plasmid: P925C / Gene (production host): DEF / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0A6K3, EC: 3.5.1.31
#2: Protein/peptide PROTEIN (MET-ALA-SER)


Mass: 307.367 Da / Num. of mol.: 3 / Source method: obtained synthetically / Details: THE PROTEIN WAS CHEMICALLY SYNTHESIZED
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.84 Å3/Da / Density % sol: 57 %
Crystal growpH: 7.4
Details: SEE: D.GROCHE,A.BECKER,I.SCHLICHTING,W.KABSCH, S.SCHULTZ,A.F.V.WAGNER (1998) BIOCHEM.BIOPHYS.RES.COMM. 246, 342, pH 7.4
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Groche, D., (1998) Biochem.Biophys.Res.Comm., 246, 342.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulfate1reservoir
20.2 MMOPS-NH31reservoir
310 mMTCEP1reservoir
430 mg/mlPDF1drop
51 %(w/v)PEG10001drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-18 / Wavelength: 1.5418
DetectorType: SIEMENS-NICOLET X100 / Detector: AREA DETECTOR / Date: Jun 15, 1997 / Details: FRANCKS DUBBLE-MIRROR OPTICS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. obs: 37363 / % possible obs: 98 % / Redundancy: 3.2 % / Biso Wilson estimate: 32.4 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.71
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 2 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 1.8 / % possible all: 93.9
Reflection
*PLUS
Num. measured all: 118387

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
XDSdata reduction
XSCALEdata scaling
X-PLOR3.851phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ICJ

1icj


Resolution: 2.1→6 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3539 10.2 %RANDOM
Rwork0.206 ---
obs0.206 34576 98.3 %-
Displacement parametersBiso mean: 37 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.26 Å
Luzzati d res low-6 Å
Luzzati sigma a0.31 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.1→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4166 0 18 160 4344
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.28
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.311.5
X-RAY DIFFRACTIONx_mcangle_it2.192
X-RAY DIFFRACTIONx_scbond_it2.252
X-RAY DIFFRACTIONx_scangle_it3.572.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.308 577 11 %
Rwork0.301 4681 -
obs--94.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARMPROTEIN.TOP
X-RAY DIFFRACTION2WAT.PARMWAT.TOP
X-RAY DIFFRACTION3PARAM.SO4TOP.SO4
X-RAY DIFFRACTION4PARAM19.IONION.TOP
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / σ(F): 0 / % reflection Rfree: 10.2 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.28
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.308 / % reflection Rfree: 11 % / Rfactor Rwork: 0.301

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