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- PDB-2w3t: Chloro complex of the Ni-Form of E.coli deformylase -

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Basic information

Entry
Database: PDB / ID: 2w3t
TitleChloro complex of the Ni-Form of E.coli deformylase
ComponentsPEPTIDE DEFORMYLASE
KeywordsHYDROLASE / PROTEIN BIOSYNTHESIS / IRON / NICKEL / METAL-BINDING
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
ETHANOL / NICKEL (II) ION / Peptide deformylase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsNgo, Y.H.T. / Palm, G.J. / Hinrichs, W.
Citation
Journal: J.Biol.Inorg.Chem. / Year: 2010
Title: Structure of the Ni(II) Complex of Escherichia Coli Peptide Deformylase and Suggestions on Deformylase Activities Depending on Different Metal(II) Centres.
Authors: Yen, N.T.H. / Bogdanovic, X. / Palm, G.J. / Kuhl, O. / Hinrichs, W.
#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.
History
DepositionNov 14, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 30, 2011Group: Database references / Derived calculations / Refinement description
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 13, 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_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_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)21,5804
Polymers21,4401
Non-polymers1403
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.080, 35.980, 67.590
Angle α, β, γ (deg.)90.00, 113.43, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2051-

HOH

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Components

#1: Protein PEPTIDE DEFORMYLASE / PDF / POLYPEPTIDE DEFORMYLASE


Mass: 21439.650 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-169
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P0A6K3, EC: 3.5.1.31
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 46.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.14 Å3/Da / Density % sol: 42.5 % / Description: NONE
Crystal growTemperature: 293 K / pH: 4 / Details: 20.5% PEG4000, 100MM NAOAC PH 4.0, 293 K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418
DetectorType: RIGAKU CCD / Detector: CCD / Date: Apr 8, 2008 / Details: OSMIC MULTILAYER
RadiationMonochromator: OSMIC MULTILAYER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.69→40 Å / Num. obs: 19326 / % possible obs: 94.2 % / Redundancy: 4.29 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18
Reflection shellResolution: 1.69→1.75 Å / Redundancy: 1.74 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 1.8 / % possible all: 56.5

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Processing

Software
NameVersionClassification
REFMAC5.5.0047refinement
d*TREKdata reduction
d*TREKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A18

2a18


Resolution: 1.69→62.02 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.744 / SU ML: 0.084 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY RESIDUAL U VALUES ARE SHOWN. CL A 1002 AND HOH A 1004 TO 1005 ALTERNATIVELY OCCUPY THE ACTIVE SITE HOH A A 1004 AND HOH A 1005 HAVE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ONLY RESIDUAL U VALUES ARE SHOWN. CL A 1002 AND HOH A 1004 TO 1005 ALTERNATIVELY OCCUPY THE ACTIVE SITE HOH A A 1004 AND HOH A 1005 HAVE BEEN REFINED WITH THE DISTANCE RESTRAINED TO 2.6 A
RfactorNum. reflection% reflectionSelection details
Rfree0.24322 1969 10.1 %RANDOM
Rwork0.21279 ---
obs0.21594 17518 94.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0.48 Å2
2--1.05 Å20 Å2
3----1.41 Å2
Refinement stepCycle: LAST / Resolution: 1.69→62.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1340 0 5 176 1521
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221382
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0781.9991860
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.35172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.76724.55968
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73415281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5961514
X-RAY DIFFRACTIONr_chiral_restr0.0730.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211023
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3891.5849
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.78721380
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.5643532
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8164.5479
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: 1.69→1.734 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.528 102
Rwork0.446 805
Refinement TLS params.Method: refined / Origin x: 9.198 Å / Origin y: 2.742 Å / Origin z: 15.584 Å
111213212223313233
T0.1272 Å2-0.0103 Å2-0.0087 Å2-0.0789 Å20.0031 Å2--0.0067 Å2
L1.9493 °20.0597 °2-0.4233 °2-0.6131 °2-0.0362 °2--2.4501 °2
S-0.0955 Å °0.1209 Å °0.0073 Å °-0.0288 Å °0.0497 Å °-0.0348 Å °0.0156 Å °0.0754 Å °0.0458 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 167
2X-RAY DIFFRACTION1A1001 - 1003
3X-RAY DIFFRACTION1A2112
4X-RAY DIFFRACTION1A2140

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