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- PDB-4eme: X-ray crystal structure and specificity of the Plasmodium falcipa... -

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Basic information

Entry
Database: PDB / ID: 4eme
TitleX-ray crystal structure and specificity of the Plasmodium falciparum malaria aminopeptidase
ComponentsM18 aspartyl aminopeptidase
KeywordsHYDROLASE / DNPEP/M18/Aminopeptidase / Protease
Function / homology
Function and homology information


aspartyl aminopeptidase / aminopeptidase activity / metallopeptidase activity / zinc ion binding
Similarity search - Function
Aminopeptidase i, Domain 2 / Aminopeptidase i, Domain 2 / Peptidase M18 / Peptidase M18, domain 2 / Aminopeptidase I zinc metalloprotease (M18) / Zn peptidases / Aminopeptidase / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
M18 aspartyl aminopeptidase
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMcGowan, S.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: X-ray crystal structure and specificity of the Plasmodium falciparum malaria aminopeptidase PfM18AAP.
Authors: Sivaraman, K.K. / Oellig, C.A. / Huynh, K. / Atkinson, S.C. / Poreba, M. / Perugini, M.A. / Trenholme, K.R. / Gardiner, D.L. / Salvesen, G. / Drag, M. / Dalton, J.P. / Whisstock, J.C. / McGowan, S.
History
DepositionApr 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: M18 aspartyl aminopeptidase
B: M18 aspartyl aminopeptidase
C: M18 aspartyl aminopeptidase
D: M18 aspartyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)263,93512
Polymers263,4124
Non-polymers5238
Water7,999444
1
A: M18 aspartyl aminopeptidase
B: M18 aspartyl aminopeptidase
C: M18 aspartyl aminopeptidase
D: M18 aspartyl aminopeptidase
hetero molecules

A: M18 aspartyl aminopeptidase
B: M18 aspartyl aminopeptidase
C: M18 aspartyl aminopeptidase
D: M18 aspartyl aminopeptidase
hetero molecules

A: M18 aspartyl aminopeptidase
B: M18 aspartyl aminopeptidase
C: M18 aspartyl aminopeptidase
D: M18 aspartyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)791,80636
Polymers790,23612
Non-polymers1,57024
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area99750 Å2
ΔGint-1368 kcal/mol
Surface area156720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.384, 200.384, 200.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213

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Components

#1: Protein
M18 aspartyl aminopeptidase


Mass: 65853.039 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PFI1570c, PfM18AAP / Production host: Escherichia coli (E. coli) / References: UniProt: Q8I2J3, aspartyl aminopeptidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.68 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.2
Details: 67% MPD, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 100K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.954 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.6→100.4 Å / Num. all: 789865 / Num. obs: 82063 / % possible obs: 100 % / Redundancy: 9.6 % / Biso Wilson estimate: 50.17 Å2 / Rmerge(I) obs: 0.248
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 6.8 % / Rmerge(I) obs: 1.439 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHASERphasing
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→55.58 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.9248 / SU R Cruickshank DPI: 0.362 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 4114 5.02 %RANDOM
Rwork0.1594 ---
obs0.1613 82024 99.79 %-
Displacement parametersBiso mean: 43.51 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: LAST / Resolution: 2.6→55.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14993 0 8 444 15445
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00915321HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1420731HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5300SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes429HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2202HARMONIC5
X-RAY DIFFRACTIONt_it15321HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion20
X-RAY DIFFRACTIONt_chiral_improper_torsion2024SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact18269SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2607 298 5.08 %
Rwork0.211 5567 -
all0.2136 5865 -
obs--99.79 %
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)
10.5115-0.0385-0.17380.2949-0.2930.51780.01450.00140.00620.08890.03580.1283-0.0351-0.0933-0.0503-0.0412-0.0070.0594-0.0314-0.0204-0.0254-62.5362-26.4314-3.5182
20.4575-0.1178-0.17580.51460.12490.447-0.0516-0.1473-0.08460.11310.00350.0490.06950.05830.0481-0.03720.00950.0177-0.01530.0029-0.0523-34.4852-50.09153.2662
30.6272-0.0488-0.04140.5126-0.03370.6208-0.0465-0.0379-0.13870.03620.02010.15250.1746-0.1060.0264-0.0857-0.09380.0652-0.116-0.01270.0458-67.6521-63.5482-7.7136
40.48020.02860.08450.25730.11050.6662-0.04960.1875-0.1414-0.13070.04190.21930.1663-0.20870.0077-0.1043-0.1913-0.087-0.042-0.08270.0482-80.6572-70.6864-50.6486
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|570 A|1001 - A|1002 }A1 - 570
2X-RAY DIFFRACTION1{ A|1 - A|570 A|1001 - A|1002 }A1001 - 1002
3X-RAY DIFFRACTION2{ B|1 - B|570 B|1001 - B|1002 }B1 - 570
4X-RAY DIFFRACTION2{ B|1 - B|570 B|1001 - B|1002 }B1001 - 1002
5X-RAY DIFFRACTION3{ C|2 - C|570 C|1001 - C|1002 }C2 - 570
6X-RAY DIFFRACTION3{ C|2 - C|570 C|1001 - C|1002 }C1001 - 1002
7X-RAY DIFFRACTION4{ D|2 - D|570 D|1001 - D|1002 }D2 - 570
8X-RAY DIFFRACTION4{ D|2 - D|570 D|1001 - D|1002 }D1001 - 1002

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