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- PDB-4dr9: Crystal structure of a peptide deformylase from synechococcus elo... -

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Basic information

Entry
Database: PDB / ID: 4dr9
TitleCrystal structure of a peptide deformylase from synechococcus elongatus in complex with actinonin
ComponentsPeptide deformylase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
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
ACTINONIN / BROMIDE ION / Peptide deformylase / Peptide deformylase
Similarity search - Component
Biological speciesSynechococcus elongatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLorimer, D. / Abendroth, J. / Craig, T. / Burgin, A. / Segall, A. / Rohwler, 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 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2013Group: Database references
Revision 1.2Jun 5, 2013Group: Database references
Revision 1.3Jul 10, 2013Group: Database references
Revision 1.4Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Apr 11, 2018Group: Data collection / Category: diffrn / diffrn_source
Revision 1.6Sep 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 / diffrn_radiation_wavelength / 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 / _diffrn_radiation_wavelength.wavelength / _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)87,53717
Polymers85,3344
Non-polymers2,20313
Water10,160564
1
A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8644
Polymers21,3341
Non-polymers5313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8644
Polymers21,3341
Non-polymers5313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9445
Polymers21,3341
Non-polymers6114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8644
Polymers21,3341
Non-polymers5313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.250, 65.780, 68.290
Angle α, β, γ (deg.)80.87, 76.82, 82.75
Int Tables number1
Space group name H-MP1

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Components

#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
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#4: Chemical
ChemComp-BB2 / ACTINONIN / 2-[(FORMYL-HYDROXY-AMINO)-METHYL]-HEPTANOIC ACID [1-(2-HYDROXYMETHYL-PYRROLIDINE-1-CARBONYL)-2-METHYL-PROPYL]-AMIDE


Mass: 385.498 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H35N3O5 / Comment: antitumor, antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / 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; 18 hour soak in reservoir solution containing 1mM actinonin

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT11.5418
SYNCHROTRONSSRL BL7-121.127092
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Feb 7, 2012 / Details: RIGAKU VARIMAX
RadiationMonochromator: RIGAKU VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.1270921
ReflectionResolution: 1.9→50 Å / Num. all: 56808 / Num. obs: 56579 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 22.89 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 17
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.02 / Num. unique all: 4200 / Rsym value: 0.49 / % possible all: 98

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Processing

Software
NameVersionClassification
JDirectordata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb deposition 1lry, modified with CCP4 program CHAINSAW

1lry


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.913 / SU B: 6.776 / SU ML: 0.104 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2852 5 %RANDOM
Rwork0.182 ---
all0.185 56808 --
obs0.185 56577 99.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20.01 Å20.4 Å2
2--0.7 Å2-0.1 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5570 0 117 564 6251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195818
X-RAY DIFFRACTIONr_bond_other_d0.0010.023968
X-RAY DIFFRACTIONr_angle_refined_deg1.6032.0177912
X-RAY DIFFRACTIONr_angle_other_deg0.92439746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0335746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.80724.375256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54315992
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1481554
X-RAY DIFFRACTIONr_chiral_restr0.0840.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216481
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021053
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: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 198 -
Rwork0.263 3908 -
obs-4114 97.93 %
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)
12.03610.4753-0.08780.9928-0.34851.32090.0232-0.1056-0.03050.0048-0.0288-0.0521-0.02430.0350.00560.0114-0.01040.00850.01940.00540.028536.56957.3052.458
21.73870.55080.71360.80540.19121.46280.08870.0274-0.07580.05720.0396-0.05370.0596-0.0008-0.12820.02150.00710.00990.0237-0.00270.034434.16125.2272.295
31.20510.10010.76591.2838-0.62812.30660.02940.11080.01920.04490.0003-0.14490.098-0.0611-0.02970.0882-0.01740.02360.05670.00790.044322.97229.70635.412
41.76040.44410.03240.9459-0.04621.66520.0244-0.06310.0366-0.03410.0137-0.06550.10680.1768-0.03810.03290.02050.01560.03990.0040.019923.38962.77334.047
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 188
2X-RAY DIFFRACTION2B6 - 187
3X-RAY DIFFRACTION3C5 - 188
4X-RAY DIFFRACTION4D5 - 188

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