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- PDB-1bs7: PEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM -

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Basic information

Entry
Database: PDB / ID: 1bs7
TitlePEPTIDE DEFORMYLASE AS NI2+ CONTAINING FORM
ComponentsPROTEIN (PEPTIDE DEFORMYLASE)
KeywordsHYDROLASE / IRON METALLOPROTEASE / PROTEIN SYNTHESIS
Function / homology
Function and homology information


co-translational protein modification / 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
NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBecker, A. / Schlichting, I. / Kabsch, W. / Groche, D. / Schultz, S. / Wagner, A.F.V.
Citation
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.
#1: 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.
#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_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_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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0478
Polymers57,6793
Non-polymers3685
Water2,360131
1
A: PROTEIN (PEPTIDE DEFORMYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2852
Polymers19,2261
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (PEPTIDE DEFORMYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4774
Polymers19,2261
Non-polymers2513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: PROTEIN (PEPTIDE DEFORMYLASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2852
Polymers19,2261
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.400, 64.000, 84.500
Angle α, β, γ (deg.)90.00, 123.00, 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 FROM ESCHERICHIA COLI IS CRYSTALLIZED AS NI2+ CONTAINING FORM
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: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


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


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


Mass: 18.015 Da / Num. of mol.: 131 / 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: 5

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56 %
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 grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mammonium sulfate11
21 %(w/v)PEG100011

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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: Jan 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: 2.5→20 Å / Num. obs: 21929 / % possible obs: 97.2 % / Redundancy: 4.1 % / Biso Wilson estimate: 44.9 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 13.3
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 2.42 / % possible all: 94.4

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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: 2.5→6 Å / Rfactor Rfree error: 0.006 / 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
Rfree0.272 1973 10 %RANDOM
Rwork0.203 ---
obs0.203 19733 97.5 %-
Displacement parametersBiso mean: 37.9 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.28 Å
Luzzati d res low-6 Å
Luzzati sigma a0.42 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 16 128 4182
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.013
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_d26.1
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.27
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.491.5
X-RAY DIFFRACTIONx_mcangle_it2.472
X-RAY DIFFRACTIONx_scbond_it2.722
X-RAY DIFFRACTIONx_scangle_it4.242.5
LS refinement shellResolution: 2.5→2.64 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 322 10.5 %
Rwork0.286 2734 -
obs--94.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PDFNI.PARMPDFNI.TOP
X-RAY DIFFRACTION2PDFNI.SCATTER
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 6 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.9 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_deg26.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.27
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
Highest resolution: 2.5 Å / Rfactor Rfree: 0.334 / % reflection Rfree: 10.5 % / Rfactor Rwork: 0.286

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