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- PDB-4dr8: Crystal structure of a peptide deformylase from Synechococcus elo... -

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Basic information

Entry
Database: PDB / ID: 4dr8
TitleCrystal structure of a peptide deformylase from Synechococcus elongatus
ComponentsPeptide deformylase
KeywordsHYDROLASE
Function / homology
Function and homology information


peptide deformylase / peptide deformylase activity / : / translation / metal ion binding
Similarity search - Function
Peptide Deformylase / Peptide deformylase / Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsLorimer, D. / Abendroth, J. / Craig, T. / Burgin, A. / Segall, A. / Rohwer, F.
CitationJournal: ISME J / Year: 2013
Title: Structure and function of a cyanophage-encoded peptide deformylase.
Authors: Frank, J.A. / Lorimer, D. / Youle, M. / Witte, P. / Craig, T. / Abendroth, J. / Rohwer, F. / Edwards, R.A. / Segall, A.M. / Burgin, A.B.
History
DepositionFeb 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2013Group: Database references
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Sep 13, 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_ref_seq_dif / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ref_seq_dif.details / _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
B: Peptide deformylase
C: Peptide deformylase
D: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,00216
Polymers85,3344
Non-polymers66712
Water17,655980
1
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5074
Polymers21,3341
Non-polymers1743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5435
Polymers21,3341
Non-polymers2094
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5074
Polymers21,3341
Non-polymers1743
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4453
Polymers21,3341
Non-polymers1112
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.400, 65.360, 69.030
Angle α, β, γ (deg.)80.01, 76.38, 81.71
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Peptide deformylase / PDF / Polypeptide deformylase


Mass: 21333.562 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC6301 / Gene: def, syc0213_d, YP_170923 / Plasmid: VCID 6622 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5N5L5, UniProt: A0A0H3JZJ4*PLUS, peptide deformylase

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Non-polymers , 5 types, 992 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CH2O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 980 / 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: 2.19 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: HAMPTON RESEARCH INDEX H12: 30% PEG 2000 MME, 150MM KBR, PH 7.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.127092 / Wavelength: 1.127092 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 31, 2012
RadiationMonochromator: single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.127092 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 104822 / Num. obs: 99872 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 13.3 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.06 / Net I/σ(I): 16.2
Reflection shellResolution: 1.55→1.59 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 3.2 / Num. unique all: 7709 / Rsym value: 0.502 / % possible all: 93

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb deposition 1lry

1lry


Resolution: 1.55→50 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.74 / SU ML: 0.052 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.083 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.194 4979 5 %RANDOM
Rwork0.162 ---
all0.164 104822 --
obs0.164 99872 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20.07 Å20.51 Å2
2--0.34 Å20.09 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5751 0 29 980 6760
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0195991
X-RAY DIFFRACTIONr_bond_other_d0.0020.024155
X-RAY DIFFRACTIONr_angle_refined_deg1.722.0028142
X-RAY DIFFRACTIONr_angle_other_deg0.974310200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8555785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65924.5280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.793151097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0361559
X-RAY DIFFRACTIONr_chiral_restr0.0970.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216689
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021086
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 343 -
Rwork0.199 6824 -
obs-7171 92.99 %
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)
11.09140.0660.23620.7679-0.44790.63730.007-0.08320.02210.02930.0041-0.0474-0.0589-0.0088-0.0110.037-0.0030.00720.0302-0.01510.016638.58356.6432.86
20.83590.23040.16920.6825-0.13670.72710.02910.0049-0.02790.04370.0144-0.03330.0048-0.0288-0.04350.03460.0151-0.00310.0203-0.00290.013234.24225.542.013
30.7991-0.17870.31050.3622-0.4291.30650.04640.06690.00850.0121-0.005-0.03550.0436-0.0492-0.04140.06280.00230.00360.0206-0.00510.029323.84129.66635.621
40.7976-0.0209-0.21410.7143-0.28171.01830.06470.04520.06990.0296-0.0056-0.0491-0.0347-0.0396-0.0590.05390.00330.00820.0073-0.00270.035624.97661.94434.511
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 189
2X-RAY DIFFRACTION2B4 - 190
3X-RAY DIFFRACTION3C4 - 188
4X-RAY DIFFRACTION4D6 - 188

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