[English] 日本語
Yorodumi
- PDB-1xfo: Crystal Structure of an archaeal aminopeptidase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1xfo
TitleCrystal Structure of an archaeal aminopeptidase
ComponentsFrv operon protein FrvX
KeywordsHYDROLASE / aminopeptidase / self-compartmentalizing / metalloprotease / dinuclear
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / metallopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M42, domain 2 / Peptidase M42, domain 2 / : / M42 glutamyl aminopeptidase / Peptidase M42 / Zn peptidases / Elongation Factor Tu (Ef-tu); domain 3 / Aminopeptidase / Beta Barrel / 3-Layer(aba) Sandwich ...Peptidase M42, domain 2 / Peptidase M42, domain 2 / : / M42 glutamyl aminopeptidase / Peptidase M42 / Zn peptidases / Elongation Factor Tu (Ef-tu); domain 3 / Aminopeptidase / Beta Barrel / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Tetrahedral aminopeptidase
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsRusso, S. / Baumann, U.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of a dodecameric tetrahedral shaped aminopeptidase
Authors: Russo, S. / Baumann, U.
History
DepositionSep 15, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 25, 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_ncs_dom_lim / 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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Frv operon protein FrvX
B: Frv operon protein FrvX
C: Frv operon protein FrvX
D: Frv operon protein FrvX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,56512
Polymers158,0424
Non-polymers5238
Water11,620645
1
A: Frv operon protein FrvX
B: Frv operon protein FrvX
C: Frv operon protein FrvX
D: Frv operon protein FrvX
hetero molecules

A: Frv operon protein FrvX
B: Frv operon protein FrvX
C: Frv operon protein FrvX
D: Frv operon protein FrvX
hetero molecules

A: Frv operon protein FrvX
B: Frv operon protein FrvX
C: Frv operon protein FrvX
D: Frv operon protein FrvX
hetero molecules


Theoretical massNumber of molelcules
Total (without water)475,69636
Polymers474,12612
Non-polymers1,57024
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area55030 Å2
ΔGint-1197 kcal/mol
Surface area129960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)158.340, 158.340, 114.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11D-412-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 4 / Auth seq-ID: 6 - 353 / Label seq-ID: 10 - 357

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsThe physiological dodecamer is generated by the three fold axis at: 1/3, 2/3, z

-
Components

#1: Protein
Frv operon protein FrvX / Frvx aminopeptidase


Mass: 39510.496 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: O59196
#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.: 645 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 400, sodium chloride, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 11, 2004 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. all: 110425 / Num. obs: 110425 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 24.3
Reflection shellResolution: 1.95→2.07 Å / Rmerge(I) obs: 0.193 / Mean I/σ(I) obs: 5.2 / % possible all: 63.5

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VHE

1vhe


Resolution: 1.96→29.92 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.948 / SU B: 6.51 / SU ML: 0.096 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.151 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 2427 2.2 %RANDOM
Rwork0.18282 ---
all0.18341 110402 --
obs0.18341 107975 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.662 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20.25 Å20 Å2
2--0.49 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 1.96→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10514 0 8 645 11167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02210711
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.96514499
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3651349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.09324.494445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.228151911
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2981554
X-RAY DIFFRACTIONr_chiral_restr0.0840.21673
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027904
X-RAY DIFFRACTIONr_nbd_refined0.1950.24889
X-RAY DIFFRACTIONr_nbtor_refined0.3030.27416
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.120.2721
X-RAY DIFFRACTIONr_metal_ion_refined0.0270.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2050.2127
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.230
X-RAY DIFFRACTIONr_mcbond_it0.3673.56965
X-RAY DIFFRACTIONr_mcangle_it0.552310850
X-RAY DIFFRACTIONr_scbond_it0.56844287
X-RAY DIFFRACTIONr_scangle_it0.9665.53649
Refine LS restraints NCS

Ens-ID: 1 / Number: 2610 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.250.5
2Bmedium positional0.140.5
3Cmedium positional0.180.5
4Dmedium positional0.170.5
1Amedium thermal0.262
2Bmedium thermal0.282
3Cmedium thermal0.262
4Dmedium thermal0.312
LS refinement shellResolution: 1.958→1.998 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.28 100 -
Rwork0.223 3752 -
obs--100 %
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)
10.7604-0.4817-0.65491.97930.51721.4388-0.0418-0.01430.0272-0.01320.0095-0.2520.01430.21430.0323-0.25210.01620.0199-0.10020.0257-0.109543.03197.58524.833
20.964-0.20070.54780.61620.21921.4961-0.03740.10350.2223-0.1176-0.0049-0.1356-0.1620.12160.0423-0.0913-0.04650.0592-0.13430.1179-0.055227.264120.8490.673
30.84560.05490.40641.5845-0.41530.7677-0.030.2766-0.0362-0.20260.0362-0.14270.00250.1609-0.0062-0.10030.00480.13740.0024-0.0232-0.145133.8786.004-8.923
41.4993-0.6273-0.58261.32060.15130.88120.0051-0.13460.10270.1122-0.0093-0.1125-0.07790.10190.0042-0.1953-0.025-0.0408-0.1786-0.0263-0.207617.817102.83456.413
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 3535 - 357
2X-RAY DIFFRACTION2BB6 - 35310 - 357
3X-RAY DIFFRACTION3CC6 - 35310 - 357
4X-RAY DIFFRACTION4DD6 - 35310 - 357

+
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