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- PDB-5i2b: Crystal structure of a peptide deformylase from Burkholderia ambi... -

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Basic information

Entry
Database: PDB / ID: 5i2b
TitleCrystal structure of a peptide deformylase from Burkholderia ambifaria with actinonin
ComponentsPeptide deformylase
KeywordsHYDROLASE / SSGCID / Burkholderia ambifaria / Peptide deformylase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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 / Peptide deformylase
Similarity search - Component
Biological speciesBurkholderia ambifaria IOP40-10 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a peptide deformylase from Burkholderia ambifaria with actinonin
Authors: Conrady, D.G. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionFeb 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 21, 2016Group: Structure summary
Revision 1.2Sep 27, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)21,6648
Polymers20,9031
Non-polymers7617
Water2,648147
1
A: Peptide deformylase
hetero molecules

A: Peptide deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,32816
Polymers41,8062
Non-polymers1,52214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area4540 Å2
ΔGint-84 kcal/mol
Surface area15480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.590, 70.250, 140.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-331-

HOH

21A-432-

HOH

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Components

#1: Protein Peptide deformylase / PDF / Polypeptide deformylase


Mass: 20902.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia ambifaria IOP40-10 (bacteria)
Gene: def, BamIOP4010DRAFT_5965 / Plasmid: BuamA.00078.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1FPK4, peptide deformylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: 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.: 1 / Source method: obtained synthetically / Formula: C19H35N3O5 / Comment: antitumor, antibiotic*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Rigaku Reagents Morpheus screen E8: 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 0.1 M MOPS/HEPES pH 7.5, 0.03M diethyleneglycol, 0.03M triethyleneglycol, 0.03M tetraethyleneglycol, 0.03M ...Details: Rigaku Reagents Morpheus screen E8: 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 0.1 M MOPS/HEPES pH 7.5, 0.03M diethyleneglycol, 0.03M triethyleneglycol, 0.03M tetraethyleneglycol, 0.03M pentaethyleneglycol; BuamA.00078.a.B1.PS02512 at 17.5 mg/ml, tray 267396 e8, puck mbf3-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→39.012 Å / Num. obs: 21509 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 21.27 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.028 / Net I/σ(I): 26.92
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.7-1.742.80.512.38199.1
1.74-1.790.442.66199.3
1.79-1.840.3163.73199.5
1.84-1.90.2644.47199.7
1.9-1.960.1936.351100
1.96-2.030.1368.96199.9
2.03-2.110.10611.9199.8
2.11-2.190.07915.49199.8
2.19-2.290.06718.7199.7
2.29-2.40.05622.64199.7
2.4-2.530.04725.66199.9
2.53-2.690.03831.23199.9
2.69-2.870.03137199.6
2.87-3.10.02445.18199.6
3.1-3.40.0258.96199.8
3.4-3.80.01776.78199.9
3.8-4.390.01693.871100
4.39-5.380.015103.591100
5.38-7.60.01796.381100
7.6-39.020.01699.6198.6

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2299refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HGW

5hgw


Resolution: 1.7→39.012 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.19
RfactorNum. reflection% reflection
Rfree0.2045 1986 9.23 %
Rwork0.1741 --
obs0.1769 21506 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 95.55 Å2 / Biso mean: 32.3057 Å2 / Biso min: 12.84 Å2
Refinement stepCycle: final / Resolution: 1.7→39.012 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 123 149 1564
Biso mean--51.6 39.01 -
Num. residues----167
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071390
X-RAY DIFFRACTIONf_angle_d0.8461877
X-RAY DIFFRACTIONf_chiral_restr0.058201
X-RAY DIFFRACTIONf_plane_restr0.007245
X-RAY DIFFRACTIONf_dihedral_angle_d13.559828
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.74250.29781300.25141376150699
1.7425-1.78960.25451280.23921353148199
1.7896-1.84230.27191410.217213891530100
1.8423-1.90170.22311170.217913851502100
1.9017-1.96970.2321320.197313971529100
1.9697-2.04860.22471310.182613691500100
2.0486-2.14180.20891590.169313801539100
2.1418-2.25470.21671530.167813671520100
2.2547-2.3960.17881480.178913791527100
2.396-2.58090.23351360.185914011537100
2.5809-2.84060.27431260.177714201546100
2.8406-3.25140.21091500.179514091559100
3.2514-4.09580.17051590.145113971556100
4.0958-39.02210.1791760.159914981674100
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)
14.47981.43820.51247.4128-4.76076.2502-0.49930.0288-0.62410.06830.0476-0.21271.0974-0.1547-0.08210.4841-0.03010.19090.1905-0.01070.341110.227979.335311.0646
21.45751.15540.02512.2239-0.7954.7209-0.0948-0.1385-0.406-0.0311-0.08-0.16680.7524-0.06160.17690.24260.00610.07810.22310.07060.22888.880883.859521.4239
36.28791.4903-0.35251.0387-0.10551.39460.0013-0.1266-0.9329-0.4604-0.4773-0.65430.43221.41440.24490.5780.19650.09290.95930.18820.859429.549486.009923.5702
47.14872.8662-1.04524.22-2.32712.2073-0.0349-0.2294-0.01750.13170.00030.02460.03930.1360.13480.17580.01450.03130.22610.0140.121614.347295.505425.3236
51.04930.33980.1597.50974.29194.0963-0.1087-0.0381-0.139-0.1990.2659-0.4490.16090.3072-0.18590.2050.02960.07280.18050.0170.190424.979793.362611.69
61.91941.5557-0.21522.5235-0.47822.99570.0865-0.4304-0.23730.2256-0.1018-0.10080.09880.02040.02880.13750.04180.02430.20060.05650.138318.182293.678324.8953
74.1411-2.6786-1.08184.64390.93372.3190.1233-0.0049-0.0095-0.4368-0.0105-0.29670.0390.3968-0.11630.27730.00580.07220.2488-0.00130.176324.160290.28353.7666
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 10 )A0 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 61 )A11 - 61
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 77 )A62 - 77
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 87 )A78 - 87
5X-RAY DIFFRACTION5chain 'A' and (resid 88 through 112 )A88 - 112
6X-RAY DIFFRACTION6chain 'A' and (resid 113 through 147 )A113 - 147
7X-RAY DIFFRACTION7chain 'A' and (resid 148 through 169 )A148 - 169

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