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- PDB-4az4: E.coli deformylase with Co(II) and hydrosulfide -

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Basic information

Entry
Database: PDB / ID: 4az4
TitleE.coli deformylase with Co(II) and hydrosulfide
ComponentsPEPTIDE DEFORMYLASE
KeywordsHYDROLASE / COBALT / HYDROGEN SULFIDE SENSOR
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 / metal 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
: / HYDROSULFURIC ACID / Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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
DepositionJun 22, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Nov 14, 2012Group: Database references
Revision 1.3Mar 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 1.4Dec 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)21,3373
Polymers21,2441
Non-polymers932
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.631, 54.631, 229.416
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
Details: C-TERMINAL HIS TAG / 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, UniProt: A0A140N556*PLUS, 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-H2S / HYDROSULFURIC ACID / HYDROGEN SULFIDE


Mass: 34.081 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsCOBALT (II) ION (CO): CO REPLACES THE NATIVE FE HYDROSULFURIC ACID (H2S): H2S IS BOUND AS ...COBALT (II) ION (CO): CO REPLACES THE NATIVE FE HYDROSULFURIC ACID (H2S): H2S IS BOUND AS HYDROSULFIDE CYSTEINE SULFENIC ACID (CSO): NO FUNCTION ASSIGNED
Sequence detailsC-TERMINAL HIS TAG

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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: 2.67 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growTemperature: 293 K / pH: 4.6
Details: 2 UL PROTEIN PLUS 2 UL (20% PEG 4000, 0.1 M NAOAC PH 4.6), 293 K. SOAKED IN 10% PEG4000, 20% PEG400, 0.1 M NAOAC PH 4.6, 293 K, FOR 1 DAY. INCUBATED IN H2S ATMOSPHERE EQUILIBRATED WITH 50 MM NA2S AT PH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 21, 2012 / Details: MIRRORS
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 20010 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.9
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.7.0027refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AL2

4al2


Resolution: 1.8→46.38 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.998 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22115 1014 5.1 %RANDOM
Rwork0.18874 ---
obs0.19035 18880 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.975 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20.49 Å20 Å2
2--0.98 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 1.8→46.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1308 0 2 82 1392
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0191355
X-RAY DIFFRACTIONr_bond_other_d0.0010.021364
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9981828
X-RAY DIFFRACTIONr_angle_other_deg0.76133146
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2495168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.55224.63869
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.33615271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3991514
X-RAY DIFFRACTIONr_chiral_restr0.0780.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211522
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02280
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_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.417 62 -
Rwork0.332 1352 -
obs--98.1 %
Refinement TLS params.Method: refined / Origin x: 2.571 Å / Origin y: -16.735 Å / Origin z: -8.175 Å
111213212223313233
T0.2534 Å20.0545 Å2-0.0746 Å2-0.2331 Å2-0.1111 Å2--0.1964 Å2
L3.7477 °20.4793 °22.0529 °2-1.3802 °21.9383 °2--6.9279 °2
S-0.2756 Å °-0.2565 Å °0.5592 Å °-0.3719 Å °-0.076 Å °0.1304 Å °-1.1337 Å °-0.0056 Å °0.3517 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 165
2X-RAY DIFFRACTION1A1164

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