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- PDB-4juq: Pseudomonas aeruginosa MetAP T2N mutant, in Mn form -

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Basic information

Entry
Database: PDB / ID: 4juq
TitlePseudomonas aeruginosa MetAP T2N mutant, in Mn form
ComponentsMethionine aminopeptidase
KeywordsHYDROLASE / T2N mutant / N-terminal methionine excision
Function / homology
Function and homology information


methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloaminopeptidase activity / transition metal ion binding / proteolysis / cytosol
Similarity search - Function
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
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsYe, Q.Z. / Lu, J.P.
CitationJournal: To be published
Title: Methionine excision captured by the structures of a methionine aminopeptidase
Authors: Lu, J.P. / Ye, Q.Z.
History
DepositionMar 25, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_auth_seq_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_conn.ptnr2_label_seq_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
B: Methionine aminopeptidase
C: Methionine aminopeptidase
D: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,36918
Polymers125,6004
Non-polymers76914
Water3,279182
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6205
Polymers31,4001
Non-polymers2204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5654
Polymers31,4001
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
C: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5654
Polymers31,4001
Non-polymers1653
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
D: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6205
Polymers31,4001
Non-polymers2204
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.593, 105.599, 133.917
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Methionine aminopeptidase


Mass: 31399.900 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: map, PA3657 / Plasmid: pGS21a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9HXY1, methionyl aminopeptidase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.27 Å3/Da / Density % sol: 45.78 %
Crystal growMethod: hanging drop vapor diffusion / pH: 7.5
Details: 100 mM HEPES, 70% MPD, pH 7.5, hanging drop vapor diffusion

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→36.87 Å / Num. obs: 58806

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→36.87 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.1981 / WRfactor Rwork: 0.1538 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8545 / SU B: 5.322 / SU ML: 0.135 / SU R Cruickshank DPI: 0.2426 / SU Rfree: 0.1981 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2293 2967 5.1 %RANDOM
Rwork0.1787 ---
obs0.1812 58652 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.36 Å2 / Biso mean: 25.7466 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8092 0 14 182 8288
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0198260
X-RAY DIFFRACTIONr_bond_other_d0.0010.027984
X-RAY DIFFRACTIONr_angle_refined_deg1.7621.9611176
X-RAY DIFFRACTIONr_angle_other_deg0.852318456
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.77551028
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31324.457368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.151151484
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2661548
X-RAY DIFFRACTIONr_chiral_restr0.10.21248
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219240
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021776
X-RAY DIFFRACTIONr_mcbond_it2.012.3724124
X-RAY DIFFRACTIONr_mcbond_other2.0052.3724123
X-RAY DIFFRACTIONr_mcangle_it2.9493.5435148
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 217 -
Rwork0.239 4007 -
all-4224 -
obs--98.85 %

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