[English] 日本語
Yorodumi
- PDB-5euf: The crystal structure of a protease from Helicobacter pylori -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5euf
TitleThe crystal structure of a protease from Helicobacter pylori
ComponentsProtease
KeywordsHYDROLASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / peptidase activity / metal ion binding
Similarity search - Function
Cytochrome Bc1 Complex; Chain A, domain 1 / Metalloenzyme, LuxS/M16 peptidase-like / Peptidase M16, zinc-binding site / Insulinase family, zinc-binding region signature. / Peptidase M16, C-terminal / Peptidase M16 inactive domain / Peptidase M16, N-terminal / Insulinase (Peptidase family M16) / Metalloenzyme, LuxS/M16 peptidase-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsTan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: The crystal structure of a protease from Helicobacter pylori
Authors: Tan, K. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references / Structure summary
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3938
Polymers95,9472
Non-polymers4466
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-113 kcal/mol
Surface area33380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.159, 50.266, 147.889
Angle α, β, γ (deg.)90.00, 94.86, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-609-

HOH

-
Components

#1: Protein Protease


Mass: 47973.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: pqqE, HPHPH19_0674 / Plasmid: pMCSG53 / Cell line (production host): BL21(DE3)magic / Production host: Escherichia coli (E. coli)
References: UniProt: I9VHL9, Hydrolases; Acting on peptide bonds (peptidases)
#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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59.21 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M Calcium Acetate, 0.1M HEPES:NaOH, 10% (w/v) PEG8000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918, 0.97940
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 5, 2014
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979181
20.97941
ReflectionResolution: 2.8→48 Å / Num. all: 27514 / Num. obs: 27514 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.124 / Net I/σ(I): 9
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 1.6 / % possible all: 92.1

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 2.8→47.803 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2445 1191 5.08 %Random selection
Rwork0.1864 ---
obs0.1894 23449 82.16 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→47.803 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6476 0 16 29 6521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026624
X-RAY DIFFRACTIONf_angle_d0.5988981
X-RAY DIFFRACTIONf_dihedral_angle_d11.5972373
X-RAY DIFFRACTIONf_chiral_restr0.0231018
X-RAY DIFFRACTIONf_plane_restr0.0031154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.91210.3671720.25221408X-RAY DIFFRACTION47
2.9121-3.04460.3315860.251821X-RAY DIFFRACTION62
3.0446-3.20510.2981050.25322197X-RAY DIFFRACTION73
3.2051-3.40590.31221660.232499X-RAY DIFFRACTION84
3.4059-3.66870.26731890.19712789X-RAY DIFFRACTION96
3.6687-4.03780.25541540.18022894X-RAY DIFFRACTION96
4.0378-4.62160.17771250.14892923X-RAY DIFFRACTION95
4.6216-5.82110.21471470.15632872X-RAY DIFFRACTION94
5.8211-47.80980.20741470.18122855X-RAY DIFFRACTION91
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)
10.39540.3711-0.02860.88150.5590.64740.17120.4909-0.0918-0.2197-0.22010.02730.25430.59030.09760.56050.30990.08261.16980.03650.30654.323-0.208278.9429
22.95060.7182-0.00643.08661.26252.6603-0.05450.64020.2144-0.6279-0.1715-0.3376-0.51660.46740.26040.35670.1287-0.04110.44130.09160.206449.222611.025399.2512
30.66990.5004-0.87420.4556-0.50161.3896-0.04380.44570.2459-0.2491-0.0766-0.139-0.56040.4506-0.43520.4753-0.04670.04711.01250.27740.316554.965416.904888.3518
42.91521.1970.55090.49620.30741.24820.06120.57080.2682-0.0139-0.1905-0.0466-0.36520.20440.15710.3770.1294-0.02180.25240.08140.173235.118510.7303102.6147
50.37130.5172-0.01380.7309-0.16561.02910.16670.6136-0.0515-0.0256-0.1198-0.2013-0.03520.60490.04480.35330.1340.02880.78750.08220.250254.31234.351895.1045
61.77070.22450.07010.25110.58741.54460.04440.88050.1315-0.4619-0.32190.1931-0.5556-0.38840.1620.52040.2102-0.10170.5889-0.12180.256123.2216.137591.853
72.27740.1066-0.84520.88750.98662.50650.00420.4420.1469-0.2479-0.09910.0989-0.3418-0.50740.54290.48480.2055-0.10350.511-0.1430.183526.27657.711493.2422
80.36490.50670.8081.42370.50272.3829-0.06530.6947-0.2247-0.2404-0.2087-0.00360.1014-0.17540.12550.42880.08070.00830.747-0.20880.280327.5302-2.279586.1336
91.96460.01480.44020.9357-0.53972.28180.1265-0.4576-0.20750.0353-0.1667-0.06450.09940.14520.05140.1925-0.0055-0.0020.1720.12650.233849.30091.517136.9492
101.6653-0.4080.48270.6840.0641.87310.0902-0.0453-0.0522-0.053-0.207-0.06430.08310.01930.09020.2055-0.00150.02430.0235-0.00680.221438.51967.1652127.0162
111.7346-0.3851-0.33191.20310.43261.974-0.0385-0.17770.0550.2107-0.20690.01510.1088-0.32630.21250.20260.02160.00670.1725-0.09680.289322.830212.7926132.9162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 30 through 62 )
2X-RAY DIFFRACTION2chain 'A' and (resid 63 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 162 )
4X-RAY DIFFRACTION4chain 'A' and (resid 163 through 192 )
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 262 )
6X-RAY DIFFRACTION6chain 'A' and (resid 263 through 319 )
7X-RAY DIFFRACTION7chain 'A' and (resid 320 through 347 )
8X-RAY DIFFRACTION8chain 'A' and (resid 348 through 444 )
9X-RAY DIFFRACTION9chain 'B' and (resid 29 through 162 )
10X-RAY DIFFRACTION10chain 'B' and (resid 163 through 312 )
11X-RAY DIFFRACTION11chain 'B' and (resid 313 through 444 )

+
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