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- PDB-4al3: peptide deformylase (Co-form) with mercaptoethanol -

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Basic information

Entry
Database: PDB / ID: 4al3
Titlepeptide deformylase (Co-form) with mercaptoethanol
ComponentsPEPTIDE DEFORMYLASE
KeywordsHYDROLASE / OXIDATION-REDUCTION
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
BETA-MERCAPTOETHANOL / : / Peptide deformylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsPalm, G.J. / Hinrichs, W.
CitationJournal: Inorg.Chem. / Year: 2012
Title: A Fret Enzyme-Based Probe for Monitoring Hydrogen Sulfide.
Authors: Strianese, M. / Palm, G.J. / Milione, S. / Kuhl, O. / Hinrichs, W. / Pellecchia, C.
History
DepositionFeb 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Other
Revision 1.2Oct 31, 2012Group: Database references
Revision 1.3Nov 14, 2012Group: Database references
Revision 1.4Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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_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_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

Downloads & links

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Assembly

Deposited unit
A: PEPTIDE DEFORMYLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4174
Polymers21,2441
Non-polymers1733
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.630, 55.630, 229.340
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein PEPTIDE DEFORMYLASE / PDF / POLYPEPTIDE DEFORMYLASE


Mass: 21244.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21(DE3) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P0A6K3, peptide deformylase
#2: Chemical ChemComp-CO / COBALT (II) ION


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCOBALT (II) ION (CO): REPLACES NATIVE DIVALENT FE BETA-MERCAPTOETHANOL (BME): BOUND TO CO AS THIOLATE

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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: 2.42 Å3/Da / Density % sol: 49.1 %
Description: REFLECTIONS FROM 2.30 - 2.21 A REMOVED BECAUSE OF ICE RING
Crystal growTemperature: 293 K / pH: 6
Details: 20.5% PEG 4000, 100 MM NA-ACETATE PH 4.0, 293 K. TRANSFERRED TO 20% PEG, 50 MM ACETATE PH 6.0, THEN SOAKED WITH 10 MM MERCAPTOETHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 25, 2010 / Details: MIRRORS
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.98→20 Å / Num. obs: 13528 / % possible obs: 88 % / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.7
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 6.3 / % possible all: 56

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLM7.0.4data reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W3T

2w3t


Resolution: 1.98→48.18 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.896 / SU B: 15.129 / SU ML: 0.177 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CO - BME S2 DISTANCE WAS RESTRAINED TO 2.30 ANGSTROM, ESD 0.10 A.
RfactorNum. reflection% reflectionSelection details
Rfree0.27582 611 4.9 %RANDOM
Rwork0.21348 ---
obs0.21645 11804 79.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 54.616 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.98→48.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 6 98 1401
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191331
X-RAY DIFFRACTIONr_bond_other_d0.0010.02944
X-RAY DIFFRACTIONr_angle_refined_deg1.4012.0011793
X-RAY DIFFRACTIONr_angle_other_deg0.95132313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9855164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78824.77667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.2815266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.3861513
X-RAY DIFFRACTIONr_chiral_restr0.0750.2207
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211454
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02239
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded12.86951
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.357 24 -
Rwork0.336 467 -
obs--48.09 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.00360.7696-0.86393.33112.97357.46390.2838-0.07420.20740.0248-0.63440.4954-0.7189-0.90430.35070.14930.01010.06740.1896-0.14280.146818.052-5.04731.395
216.4115-1.2864-9.90347.37723.75921.2321-0.3960.09230.785-1.1286-0.37272.52890.7219-3.46420.76870.3169-0.1552-0.37851.3169-0.37021.07352.748-16.67618.856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 146
2X-RAY DIFFRACTION1A1163 - 1165
3X-RAY DIFFRACTION2A147 - 164

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