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- PDB-3s6b: Crystal structure of methionine aminopeptidase 1b from Plasmodium... -

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Basic information

Entry
Database: PDB / ID: 3s6b
TitleCrystal structure of methionine aminopeptidase 1b from Plasmodium Falciparum, PF10_0150
ComponentsMethionine aminopeptidase
KeywordsHYDROLASE / malaria / proteolysis / "pita bread" fold / peptidase / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


: / protein modification process => GO:0036211 / methionyl aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / proteolysis / metal ion binding / cytoplasm
Similarity search - Function
MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like ...MYND-like zinc finger / zf-MYND-like zinc finger, mRNA-binding / Methionine aminopeptidase subfamily 1 signature. / Peptidase M24A, methionine aminopeptidase, subfamily 1 / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / Methionine aminopeptidase 1b
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWernimont, A.K. / Artz, J.D. / Crombet, L. / Lew, J. / Weadge, J. / Tempel, W. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. ...Wernimont, A.K. / Artz, J.D. / Crombet, L. / Lew, J. / Weadge, J. / Tempel, W. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Hui, R. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of methionine aminopeptidase 1b from Plasmodium Falciparum, PF10_0150
Authors: Wernimont, A.K. / Artz, J.D. / Crombet, L. / Lew, J. / Weadge, J. / Arrowsmith, C.H. / Edwards, A.M. / Weigelt, J. / Bountra, C. / Hui, R. / Hills, T.
History
DepositionMay 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
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_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.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_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_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: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7044
Polymers42,4641
Non-polymers2403
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.868, 52.581, 63.506
Angle α, β, γ (deg.)90.000, 116.670, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methionine aminopeptidase


Mass: 42463.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF10_0150 / Plasmid: pet28mlh / Production host: Escherichia coli (E. coli) / Strain (production host): bl21de3 / References: UniProt: Q8IJP2, methionyl aminopeptidase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.07 Å3/Da / Density % sol: 40.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 27% PEG3350, 0.2 M Ammonium Acetate, 0.1 M Tris, 2 mM TCEP, 20 % glycerol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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 RAXIS IV++ / Detector: IMAGE PLATE / Date: May 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→40 Å / Num. all: 27575 / Num. obs: 27052 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 25.7 Å2 / Rmerge(I) obs: 0.069 / Χ2: 1.75 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.9-1.932.30.6371.8110841.55678.8
1.93-1.972.50.5542.2512071.64488.8
1.97-2.012.80.48113041.54396
2.01-2.053.50.44613771.65799.9
2.05-2.093.50.39213591.59999.9
2.09-2.143.60.35313671.702100
2.14-2.193.60.30613941.656100
2.19-2.253.60.25613431.73399.9
2.25-2.323.60.21613771.71799.9
2.32-2.393.60.19613791.737100
2.39-2.483.60.18213651.829100
2.48-2.583.60.1513801.75699.9
2.58-2.73.70.11513571.732100
2.7-2.843.70.10513871.8100
2.84-3.023.70.07413721.802100
3.02-3.253.70.05913881.812100
3.25-3.583.70.04213841.87699.9
3.58-4.093.70.03713831.832100
4.09-5.153.70.03414041.78100
5.15-403.60.03314411.95999.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
JDirectordata collection
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2b3h

2b3h


Resolution: 1.95→35 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2095 / WRfactor Rwork: 0.1641 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8413 / SU B: 9.911 / SU ML: 0.125 / SU R Cruickshank DPI: 0.1816 / SU Rfree: 0.1618 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 1297 5.1 %RANDOM
Rwork0.1779 ---
obs0.1803 25316 99.3 %-
all-25494 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.83 Å2 / Biso mean: 29.862 Å2 / Biso min: 15.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.07 Å20 Å2-3.1 Å2
2---0.8 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 13 176 2968
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222992
X-RAY DIFFRACTIONr_angle_refined_deg1.4131.9524077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6425371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92624.38137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37215513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6171512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212304
X-RAY DIFFRACTIONr_mcbond_it0.6121.51809
X-RAY DIFFRACTIONr_mcangle_it1.07722980
X-RAY DIFFRACTIONr_scbond_it2.00731183
X-RAY DIFFRACTIONr_scangle_it3.1034.51097
LS refinement shellResolution: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 97 -
Rwork0.273 1640 -
all-1737 -
obs--93.89 %
Refinement TLS params.Method: refined / Origin x: 7.2306 Å / Origin y: 16.2771 Å / Origin z: 13.9547 Å
111213212223313233
T0.0163 Å20.0126 Å2-0.0043 Å2-0.0169 Å2-0.006 Å2--0.0144 Å2
L0.6576 °20.1177 °20.1291 °2-0.4896 °2-0.058 °2--0.7611 °2
S0.0013 Å °-0.0649 Å °0.0079 Å °0.0182 Å °-0.0049 Å °-0.0231 Å °0.0067 Å °-0.0064 Å °0.0036 Å °

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