[English] 日本語
Yorodumi
- PDB-4hvt: Structure of a Post-proline cleaving enzyme from Rickettsia typhi -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hvt
TitleStructure of a Post-proline cleaving enzyme from Rickettsia typhi
ComponentsPost-proline cleaving enzyme
KeywordsHYDROLASE / SSGCID / Post-proline cleaving enzyme / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / post-proline cleavage protein
Function / homology
Function and homology information


prolyl oligopeptidase / serine-type endopeptidase activity
Similarity search - Function
Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Post-proline cleaving enzyme
Similarity search - Component
Biological speciesRickettsia typhi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD, MOLECULAR REPLACEMENT / SAD / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Structure of a Post-proline cleaving enzyme from Rickettsia typhi
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID) / Abendroth, J. / Sankaran, B. / Fox III, D. / Edwards, T.E. / Staker, B.L.
History
DepositionNov 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Data collection / Category: pdbx_diffrn_reflns_shell / Item: _pdbx_diffrn_reflns_shell.percent_possible_obs
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Post-proline cleaving enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,6709
Polymers82,2271
Non-polymers4438
Water13,439746
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)199.590, 73.280, 55.460
Angle α, β, γ (deg.)90.000, 98.520, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1386-

HOH

-
Components

#1: Protein Post-proline cleaving enzyme / RityA.17583.b


Mass: 82226.664 Da / Num. of mol.: 1 / Fragment: N-terminal truncation (UNP residues 19-720)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rickettsia typhi (bacteria) / Strain: ATCC VR-144 / Wilmington / Gene: ppcE, RT0165 / Plasmid: RityA.17583.b.B2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q68XJ3, prolyl oligopeptidase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 746 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4450
22.2846
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2901vapor diffusion, sitting drop8.5Microlyic MCSG1 screen b10: 24% PEG 4000, 20% Glycerol, 160mM Magnesium Chloride, 80mM Tris:HCl pH 8.5; RityA17583bB2.PS01616 at 26.6mg/ml, cryo: EG; SG C2; for phasing crystal 2 was used SG P21, VAPOR DIFFUSION, SITTING DROP, temperature 290K
2902vapor diffusion, sitting drop7.5Microlyic MCSG1 screen c5: 20% PEG 3350, 200mM Magnesium acetate; RityA17583bB2.PS01616 at 26.6mg/ml, for phasing a crystal was soaked in reservoir + 20% EG with 2.5M sodium iodide (final 500mM NaI) for 1 minute, this sample is from a differet space group (P21) than crystal 1, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONALS 5.0.110.9774
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.5418
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDOct 14, 2012
RIGAKU SATURN 944+2CCDOct 17, 2012
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystal, cylindrically bent, Si(220)SINGLE WAVELENGTHMx-ray1
2RIGAKU VariMaxSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97741
21.54181
ReflectionNumber: 305759 / Rmerge(I) obs: 0.05 / D res high: 2.1 Å / Num. obs: 84077 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)IDRmerge(I) obs
9.395091095.510.03
6.649.39170298.710.033
5.426.64219798.910.037
4.75.42267499.610.033
4.24.7300599.810.032
3.834.2332899.910.037
3.553.83361999.810.039
3.323.55387799.910.042
3.133.32417210010.041
2.973.13436810010.047
2.832.97461799.910.053
2.712.83475710010.062
2.62.71508499.910.078
2.512.6515210010.072
2.422.51541410010.081
2.352.42562299.910.084
2.282.35577099.910.097
2.212.28583999.510.126
2.152.21615699.910.11
2.12.1558149310.111
ReflectionResolution: 1.7→50 Å / Num. all: 87031 / Num. obs: 86126 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 23.221 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 16.86
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.740.4933.423080663481,298
1.74-1.790.3994.222969561291,298.5
1.79-1.840.325.152912559851,298.6
1.84-1.90.2526.532822557921,298.6
1.9-1.960.1968.32736456391,298.7
1.96-2.030.15710.122652454581,298.6
2.03-2.110.12912.082566952861,299
2.11-2.190.10414.412468751081,299.1
2.19-2.290.08916.322370048991,298.8
2.29-2.40.07917.892256546691,299.3
2.4-2.530.07119.622148744671,299
2.53-2.690.06222.092039142361,299.7
2.69-2.870.05524.671900439781,299.4
2.87-3.10.04528.471755636941,299.6
3.1-3.40.03833.061617534241,299.5
3.4-3.80.03337.541439831031,299.5
3.8-4.390.03238.851233527371,299.3
4.39-5.380.02841.761117323351,299.7
5.38-7.60.0338.87871218181,299.5
7.6-500.02542.91475110211,298.7

-
Phasing

Phasing
Method
SAD
molecular replacement
Phasing MADD res high: 2.1 Å / D res low: 46.03 Å / FOM : 0.416 / FOM acentric: 0.429 / FOM centric: 0.128 / Reflection: 43000 / Reflection acentric: 41043 / Reflection centric: 1776
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å20 Å
Translation3.5 Å20 Å

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
JDirectordata collection
XDSdata reduction
RefinementMethod to determine structure: SAD, MOLECULAR REPLACEMENT
Starting model: An initial model was obtained from iodide SAD phasing using crystal 2 (P21). The initial model was then used as search model for C2 high resolution data set, crystal 1.

Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / WRfactor Rfree: 0.1996 / WRfactor Rwork: 0.1636 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8714 / SU B: 3.886 / SU ML: 0.067 / SU R Cruickshank DPI: 0.099 / SU Rfree: 0.1011 / Isotropic thermal model: isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 4322 5 %RANDOM
Rwork0.1704 ---
all0.1723 87031 --
obs0.1723 81804 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.98 Å2 / Biso mean: 19.2341 Å2 / Biso min: 7.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20.54 Å2
2--0.79 Å20 Å2
3----0.96 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5510 0 26 746 6282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.025739
X-RAY DIFFRACTIONr_bond_other_d0.0010.025324
X-RAY DIFFRACTIONr_angle_refined_deg1.6831.9517804
X-RAY DIFFRACTIONr_angle_other_deg0.85312259
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6875712
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.67324.583264
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87915945
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9971519
X-RAY DIFFRACTIONr_chiral_restr0.1040.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216514
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021357
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 331 -
Rwork0.228 5994 -
all-6325 -
obs-6348 98.03 %
Refinement TLS params.Method: refined / Origin x: 23.725 Å / Origin y: 61.672 Å / Origin z: 16.053 Å
111213212223313233
T0.0536 Å20.0113 Å2-0.0666 Å2-0.0092 Å2-0.0115 Å2--0.085 Å2
L0.4637 °20.0058 °20.2563 °2-0.529 °2-0.0524 °2--0.5823 °2
S-0.0773 Å °-0.0259 Å °0.0877 Å °-0.015 Å °0.027 Å °0.0072 Å °-0.0651 Å °-0.0668 Å °0.0504 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 710
2X-RAY DIFFRACTION1A801 - 808

+
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://pdbjlvh1.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