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- PDB-3mx6: Crystal structure of methionine aminopeptidase from Rickettsia pr... -

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Basic information

Entry
Database: PDB / ID: 3mx6
TitleCrystal structure of methionine aminopeptidase from Rickettsia prowazekii bound to methionine
ComponentsMethionine aminopeptidase
KeywordsHYDROLASE / Seattle Structural Genomics Center for Infectious Disease / SSGCID / aminopeptidase / protease / epidermic typhus / lice-born pathogen
Function / homology
Function and homology information


methionyl aminopeptidase / initiator methionyl aminopeptidase activity / metalloaminopeptidase activity / proteolysis / metal ion binding
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 / Methionine aminopeptidase
Similarity search - Component
Biological speciesRickettsia prowazekii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Bioorg.Med.Chem. / Year: 2017
Title: Rickettsia prowazekii methionine aminopeptidase as a promising target for the development of antibacterial agents.
Authors: Helgren, T.R. / Chen, C. / Wangtrakuldee, P. / Edwards, T.E. / Staker, B.L. / Abendroth, J. / Sankaran, B. / Housley, N.A. / Myler, P.J. / Audia, J.P. / Horn, J.R. / Hagen, T.J.
History
DepositionMay 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 8, 2017Group: Database references
Revision 1.3Feb 15, 2017Group: Database references
Revision 1.4Sep 6, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Mar 11, 2026Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / cell / chem_comp / chem_comp_atom / diffrn / entity / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_distant_solvent_atoms / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_refine_tls_group / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _cell.angle_beta / _chem_comp.formula ..._cell.angle_beta / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _diffrn.pdbx_serial_crystal_experiment / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _pdbx_contact_author.fax / _pdbx_contact_author.id / _pdbx_contact_author.identifier_ORCID / _pdbx_contact_author.name_salutation / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_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.value / _pdbx_struct_sheet_hbond.sheet_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.occupancy_max / _refine.occupancy_min / _refine.overall_FOM_work_R_set / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.overall_SU_R_Cruickshank_DPI / _refine.overall_SU_R_free / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_solvent_ion_probe_radii / _refine.pdbx_solvent_shrinkage_radii / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version / _struct.pdbx_CASP_flag / _struct_asym.entity_id / _struct_conf.pdbx_PDB_helix_id / _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.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_mon_prot_cis.pdbx_omega_angle / _struct_ref.db_code / _struct_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id
Description: Ligand identity
Details: The metal in the original protein used for crystallization was experimentally determined and found to be different from that originally modelled.
Provider: author / Type: Coordinate replacement

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,76210
Polymers58,1952
Non-polymers5688
Water13,079726
1
A: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3815
Polymers29,0971
Non-polymers2844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methionine aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3815
Polymers29,0971
Non-polymers2844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.370, 67.550, 80.890
Angle α, β, γ (deg.)90.000, 97.429, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Methionine aminopeptidase / MAP / Peptidase M


Mass: 29097.283 Da / Num. of mol.: 2 / Fragment: unp residues 3-259
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia prowazekii (bacteria) / Gene: map, RP824 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9ZCD3, methionyl aminopeptidase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO2S
#4: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 726 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M sodium sulfate, 0.1 M BisTris propane, 20% PEG 3350, 20% ethylene glycol as cryo-protectant, 25.2 mg/mL protein, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 30, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 58037 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 19.463 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 21.52
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 5.9 / Num. measured obs: 12352 / Num. unique obs: 3587 / % possible all: 82.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 38.74 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.15 Å
Translation2.5 Å40.15 Å

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0430 (refmacat 0.4.105)refinement
XSCALEdata scaling
PHASER2.1.4phasing
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3MR1

3mr1


Resolution: 1.7→19.983 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.828 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.103
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1985 2932 5.057 %RANDOM
Rwork0.1597 55045 --
all0.162 ---
obs-57977 97.794 %-
Solvent computationIon probe radii: 1 Å / Shrinkage radii: 1 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.205 Å2
Baniso -1Baniso -2Baniso -3
1-0.002 Å20 Å2-0.002 Å2
2--0.001 Å20 Å2
3----0.002 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4086 0 6 726 4818
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0174242
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164023
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.8075747
X-RAY DIFFRACTIONr_angle_other_deg0.4431.5719301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4085.146549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.53710733
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.82910179
X-RAY DIFFRACTIONr_chiral_restr0.0610.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02922
X-RAY DIFFRACTIONr_nbd_refined0.2050.2799
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1720.23601
X-RAY DIFFRACTIONr_nbtor_refined0.1720.22110
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.22110
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2483
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0590.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1060.21
X-RAY DIFFRACTIONr_nbd_other0.1290.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1390.225
X-RAY DIFFRACTIONr_mcbond_it1.1691.122099
X-RAY DIFFRACTIONr_mcbond_other1.1641.1212099
X-RAY DIFFRACTIONr_mcangle_it1.782.0092622
X-RAY DIFFRACTIONr_mcangle_other1.7882.0092623
X-RAY DIFFRACTIONr_scbond_it2.3241.4022143
X-RAY DIFFRACTIONr_scbond_other2.3231.4032141
X-RAY DIFFRACTIONr_scangle_it3.5832.4283118
X-RAY DIFFRACTIONr_scangle_other3.5822.433119
X-RAY DIFFRACTIONr_lrange_it5.23313.4294996
X-RAY DIFFRACTIONr_lrange_other5.06112.734885
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.7-1.7440.2341960.18533670.18843370.9720.98282.15360.158
1.744-1.7910.2242190.17937000.18242520.9680.98392.16840.152
1.791-1.8430.2321870.17838650.18141010.9670.98298.80520.152
1.843-1.8990.1861950.16437680.16639720.9770.98399.77340.143
1.899-1.9610.2091790.16236920.16438780.9720.98399.81950.142
1.961-2.0290.1871730.15835510.15937300.9780.98499.83910.142
2.029-2.1040.2071680.15834840.1636620.9730.98599.72690.144
2.104-2.1890.1832090.14932690.15134840.9780.98699.82780.141
2.189-2.2860.2021630.16431820.16633500.9750.98499.85070.154
2.286-2.3960.1651590.14730100.14831750.9810.98799.8110.139
2.396-2.5230.191560.15529030.15730640.9750.98599.83680.147
2.523-2.6730.2071750.14626920.1528710.9750.98799.86070.143
2.673-2.8540.1981390.14625680.14927160.9740.98699.66860.144
2.854-3.0780.2031250.16224140.16425440.9730.98499.80350.165
3.078-3.3640.191120.15922650.16123830.9780.98599.74820.167
3.364-3.7470.2031150.15419870.15721130.9760.98599.47940.165
3.747-4.3020.193840.14817960.1518850.980.98699.73470.162
4.302-5.2090.194800.15815380.1616280.9850.98899.38570.18
5.209-7.1280.243600.20212280.20412900.9750.98299.8450.221
7.128-19.9830.154380.1797660.1778060.9830.98599.75190.203

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