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- PDB-1rqc: Crystals of peptide deformylase from Plasmodium falciparum with t... -

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Basic information

Entry
Database: PDB / ID: 1rqc
TitleCrystals of peptide deformylase from Plasmodium falciparum with ten subunits per asymmetric unit reveal critical characteristics of the active site for drug design
Componentsformylmethionine deformylase
KeywordsHYDROLASE
Function / homology
Function and homology information


apicoplast / co-translational protein modification / N-terminal protein amino acid modification / peptide deformylase / peptide deformylase activity / ferrous iron binding / translation / mitochondrion / membrane
Similarity search - Function
Peptide Deformylase / Peptide deformylase / Peptide deformylase / Peptide deformylase superfamily / Polypeptide deformylase / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Peptide deformylase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsRobien, M.A. / Nguyen, K.T. / Kumar, A. / Hirsh, I. / Turley, S. / Pei, D. / Hol, W.G.
Citation
Journal: Protein Sci. / Year: 2004
Title: An improved crystal form of Plasmodium falciparum peptide deformylase
Authors: Robien, M.A. / Nguyen, K.T. / Kumar, A. / Hirsh, I. / Turley, S. / Pei, D. / Hol, W.G.
#1: Journal: Structure / Year: 2002
Title: Crystals of Peptide Deformylase from Plasmodium falciparum reveal critical characteristics of the active site for drug design
Authors: Kumar, A. / Nguyen, K.T. / Srivathsan, S. / Ornstein, B. / Turley, S. / Hirsh, I. / Pei, D. / Hol, W.G.
History
DepositionDec 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: formylmethionine deformylase
B: formylmethionine deformylase
C: formylmethionine deformylase
D: formylmethionine deformylase
E: formylmethionine deformylase
F: formylmethionine deformylase
G: formylmethionine deformylase
H: formylmethionine deformylase
I: formylmethionine deformylase
J: formylmethionine deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,07020
Polymers220,48010
Non-polymers58910
Water2,684149
1
A: formylmethionine deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1072
Polymers22,0481
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: formylmethionine deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1072
Polymers22,0481
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: formylmethionine deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1072
Polymers22,0481
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: formylmethionine deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1072
Polymers22,0481
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: formylmethionine deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1072
Polymers22,0481
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: formylmethionine deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1072
Polymers22,0481
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: formylmethionine deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1072
Polymers22,0481
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: formylmethionine deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1072
Polymers22,0481
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: formylmethionine deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1072
Polymers22,0481
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: formylmethionine deformylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1072
Polymers22,0481
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.263, 121.263, 177.272
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: LYS / Refine code: 6

Dom-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1HISAA66 - 2434 - 181
2HISBB66 - 2434 - 181
3ALACC66 - 2334 - 171
4GLUDD66 - 2384 - 176
5LEUEE66 - 2404 - 178
6GLUFF66 - 2374 - 175
7SERGG66 - 2364 - 174
8GLUHH66 - 2384 - 176
9SERII66 - 2364 - 174
10SERJJ66 - 2364 - 174
DetailsThe asymmetric unit contains 10 monomers. The biologically active unit is the monomer

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Components

#1: Protein
formylmethionine deformylase /


Mass: 22048.049 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: PDF / Plasmid: PET29B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8I372
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.95 Å3/Da / Density % sol: 58.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Tris, sodium chloride, magnesium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9794, 0.9792, 0.96400
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2001
RadiationMonochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97921
30.9641
ReflectionResolution: 2.5→25 Å / Num. obs: 77903 / % possible obs: 89.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 53.229 Å2 / Rsym value: 0.096 / Net I/σ(I): 10.6
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 4631 / Rsym value: 0.482 / % possible all: 43.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
SHARPphasing
DMphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.842 / SU B: 15.051 / SU ML: 0.285 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.457
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.27698 2624 5.1 %RANDOM
Rwork0.22493 ---
obs0.22755 49121 82.49 %-
all-49121 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.875 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å20 Å2
2--0.47 Å20 Å2
3----0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14339 0 10 149 14498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02214585
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.96619582
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.98751720
X-RAY DIFFRACTIONr_chiral_restr0.10.22152
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210692
X-RAY DIFFRACTIONr_nbd_refined0.2610.36438
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2260.5386
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3070.3125
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3340.510
X-RAY DIFFRACTIONr_mcbond_it1.07648633
X-RAY DIFFRACTIONr_mcangle_it2.085814118
X-RAY DIFFRACTIONr_scbond_it1.81685952
X-RAY DIFFRACTIONr_scangle_it3.129125464
Refine LS restraints NCS

Ens-ID: 1 / Number: 1391 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.395
2Bloose positional0.385
3Cloose positional0.485
4Dloose positional0.385
5Eloose positional0.385
6Floose positional0.385
7Gloose positional0.395
8Hloose positional0.45
9Iloose positional0.45
10Jloose positional0.325
1Aloose thermal6.7810
2Bloose thermal3.6610
3Cloose thermal7.8110
4Dloose thermal4.3510
5Eloose thermal4.2410
6Floose thermal8.4610
7Gloose thermal6.1910
8Hloose thermal3.5810
9Iloose thermal3.910
10Jloose thermal3.9910
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.346 118
Rwork0.292 2186

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