[English] 日本語
Yorodumi
- PDB-2bwv: His361Ala Escherichia coli Aminopeptidase P -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bwv
TitleHis361Ala Escherichia coli Aminopeptidase P
ComponentsAMINOPEPTIDASE P
KeywordsHYDROLASE / METALLOENZYME / 'PITA-BREAD' ENZYME / PROLINE-SPECIFIC ENZYME / MANGANESE ENZYME
Function / homology
Function and homology information


Xaa-Pro aminopeptidase / metalloexopeptidase activity / metalloaminopeptidase activity / aminopeptidase activity / manganese ion binding / protein homotetramerization / protein-containing complex / proteolysis / identical protein binding / cytosol
Similarity search - Function
Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / : / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase ...Aminopeptidase P, N-terminal / Aminopeptidase P, N-terminal domain / Aminopeptidase P, N-terminal domain / : / Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site / Aminopeptidase P and proline dipeptidase signature. / Creatine Amidinohydrolase; Chain A, domain 1 / Creatinase/prolidase N-terminal domain / Creatinase/Aminopeptidase P/Spt16, N-terminal / Peptidase M24, methionine aminopeptidase / Creatine Amidinohydrolase / Creatinase/methionine aminopeptidase superfamily / Peptidase M24 / Metallopeptidase family M24 / Creatinase/aminopeptidase-like / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Xaa-Pro aminopeptidase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGraham, S.C. / Guss, J.M.
CitationJournal: Biochemistry / Year: 2006
Title: Kinetic and Crystallographic Analysis of Mutant Escherichia Coli Aminopeptidase P: Insights Into Substrate Recognition and the Mechanism of Catalysis.
Authors: Graham, S.C. / Lilley, P.E. / Lee, M. / Schaeffer, P.M. / Kralicek, A.V. / Dixon, N.E. / Guss, J.M.
History
DepositionJul 19, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Data collection / Database references / Category: citation / Item: _citation.page_last
Revision 1.4May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AMINOPEPTIDASE P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8384
Polymers49,6931
Non-polymers1453
Water11,692649
1
A: AMINOPEPTIDASE P
hetero molecules

A: AMINOPEPTIDASE P
hetero molecules

A: AMINOPEPTIDASE P
hetero molecules

A: AMINOPEPTIDASE P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)199,35316
Polymers198,7724
Non-polymers58112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+4/31
crystal symmetry operation10_666-y+1,-x+1,-z+4/31
Buried area12400 Å2
ΔGint-20 kcal/mol
Surface area85590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.339, 177.339, 96.475
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422

-
Components

#1: Protein AMINOPEPTIDASE P / AMINOPEPTIDASE P / X-PRO AMINOPEPTIDASE / AMINOPEPTIDASE P II / APP-II / AMINOACYLPROLINE AMINOPEPTIDASE


Mass: 49692.996 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: AN1459 / Plasmid: PPL670/H361A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): AN1459 / References: UniProt: P15034, Xaa-Pro aminopeptidase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 361 TO ALA
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.4 Å3/Da / Density % sol: 71.9 %
Description: STARTING MODEL WAS STRIPPED OF HETATMS AND MULTIPLE CONFORMERS
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: HANGING DROP VAPOUR DIFFUSION AT 4C. 2 UL 6 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 28 % PEG 4K, 0.1 M TRIS PH 8.5. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 10% MPD AND 1 MM MNCL2 ...Details: HANGING DROP VAPOUR DIFFUSION AT 4C. 2 UL 6 MG/ML APPRO PLUS 2 UL RESERVOIR SOLUTION: 28 % PEG 4K, 0.1 M TRIS PH 8.5. SOAKED IN RESERVOIR SOLUTION SUPPLEMENTED WITH 10% MPD AND 1 MM MNCL2 FOR 1 HR AT 4C PRIOR TO CRYOCOOLING.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200H / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 5, 2005 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→65.23 Å / Num. obs: 96986 / % possible obs: 99.4 % / Observed criterion σ(I): 6 / Redundancy: 6 % / Biso Wilson estimate: 22.44 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.7
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.8 / % possible all: 99.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WL9

1wl9


Resolution: 1.7→154.3 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 2.188 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.165 2938 3 %RANDOM
Rwork0.15 ---
obs0.15 94042 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å2-0.04 Å20 Å2
2---0.08 Å20 Å2
3---0.12 Å2
Refinement stepCycle: LAST / Resolution: 1.7→154.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 3 649 4147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223628
X-RAY DIFFRACTIONr_bond_other_d0.0010.023303
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.9564928
X-RAY DIFFRACTIONr_angle_other_deg0.80337662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9025457
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.82823.67188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.77215623
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3141534
X-RAY DIFFRACTIONr_chiral_restr0.0740.2538
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024113
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02761
X-RAY DIFFRACTIONr_nbd_refined0.210.2728
X-RAY DIFFRACTIONr_nbd_other0.1760.23406
X-RAY DIFFRACTIONr_nbtor_refined0.1720.21737
X-RAY DIFFRACTIONr_nbtor_other0.0790.22044
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2407
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.274
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.02722903
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.26533574
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.85741630
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.59461345
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.364 219
Rwork0.302 6851
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)
10.8904-0.06510.38040.6338-0.0750.5866-0.06350.02440.13830.0359-0.00180.0053-0.12970.0280.0653-0.07380.0217-0.0145-0.06980.0036-0.071160.967280.541448.4865
20.4113-0.16740.1110.5093-0.13951.03590.00940.0042-0.06290.0129-0.02210.06880.2075-0.02760.0127-0.07360.01550.0161-0.1091-0.0057-0.09767.359643.782350.6096
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 172
2X-RAY DIFFRACTION2A173 - 440

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more