[English] 日本語
Yorodumi
- PDB-3luo: Crystal Structure and functional characterization of the thermoph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3luo
TitleCrystal Structure and functional characterization of the thermophilic prolyl isomerase and chaperone SlyD
Components
  • Peptidyl-prolyl cis-trans isomerase
  • Suc-Ala-Leu-Pro-Phe-pNA
KeywordsISOMERASE / PROLYL CIS TRANS ISOMERASE / CHAPERONE FUNCTION / TWO DOMAIN PROTEIN / Ni(2+) Zn(2+) BINDING / SLYD
Function / homology
Function and homology information


peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein refolding / metal ion binding
Similarity search - Function
Chitinase A; domain 3 - #40 / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Peptidyl-prolyl cis-trans isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.55 Å
AuthorsLoew, C. / Neumann, P. / Weininger, U. / Stubbs, M.T. / Balbach, J.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal Structure Determination and Functional Characterization of the Metallochaperone SlyD from Thermus thermophilus
Authors: Loew, C. / Neumann, P. / Tidow, H. / Weininger, U. / Haupt, C. / Friedrich-Epler, B. / Scholz, C. / Stubbs, M.T. / Balbach, J.
History
DepositionFeb 18, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2014Group: Derived calculations
Revision 1.3Nov 1, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Peptidyl-prolyl cis-trans isomerase
B: Suc-Ala-Leu-Pro-Phe-pNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2526
Polymers17,9912
Non-polymers2624
Water37821
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Peptidyl-prolyl cis-trans isomerase
B: Suc-Ala-Leu-Pro-Phe-pNA
hetero molecules

A: Peptidyl-prolyl cis-trans isomerase
B: Suc-Ala-Leu-Pro-Phe-pNA
hetero molecules

A: Peptidyl-prolyl cis-trans isomerase
B: Suc-Ala-Leu-Pro-Phe-pNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,75718
Polymers53,9736
Non-polymers78512
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area6300 Å2
ΔGint-386 kcal/mol
Surface area25740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.400, 111.400, 111.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number199
Space group name H-MI213

-
Components

#1: Protein Peptidyl-prolyl cis-trans isomerase


Mass: 17400.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET-VECTOR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5SLE7, peptidylprolyl isomerase
#2: Protein/peptide Suc-Ala-Leu-Pro-Phe-pNA


Mass: 590.625 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE PEPTIDE SUBSTRATE WAS PURCHASED FROM A COMPANY.
#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.: 21 / 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: 3.2 Å3/Da / Density % sol: 61.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10MG/ML N-SUC-ALA-LEU-PRO-PHE-PNA, 2M AMMONIUM SULFATE, 5 % PEG 400, 100MM MES, PH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 12, 2009 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9841 Å / Relative weight: 1
ReflectionResolution: 2.55→20 Å / Num. all: 7658 / Num. obs: 7636 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.35 % / Biso Wilson estimate: 68.806 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.054 / Net I/σ(I): 23.77
Reflection shellResolution: 2.55→2.65 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.643 / Mean I/σ(I) obs: 3.5 / Num. measured obs: 5982 / Num. unique all: 808 / Num. unique obs: 808 / Rsym value: 0.662 / % possible all: 100

-
Processing

Software
NameVersionClassificationNB
XSCALEdata processing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
MAR345dtbdata collection
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3CGM

3cgm


Resolution: 2.55→19.693 Å / Occupancy max: 1 / Occupancy min: 0.43 / SU ML: 0.33 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1.24 / σ(I): 0 / Stereochemistry target values: ML / Details: TLS parameters have been included in refinemnt
RfactorNum. reflection% reflectionSelection details
Rfree0.235 731 5.03 %RANDOM
Rwork0.205 ---
obs0.207 7636 99.93 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 92.506 Å2 / ksol: 0.407 e/Å3
Displacement parametersBiso max: 215.89 Å2 / Biso mean: 94.308 Å2 / Biso min: 31.23 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.33 Å
Luzzati d res low-8 Å
Luzzati sigma a0.37 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.55→19.693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1160 0 4 21 1185
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0231195
X-RAY DIFFRACTIONf_angle_d0.9281614
X-RAY DIFFRACTIONf_chiral_restr0.058174
X-RAY DIFFRACTIONf_plane_restr0.004219
X-RAY DIFFRACTIONf_dihedral_angle_d18.271431
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.55-2.6090.278490.288923972100
2.609-2.6750.391480.28991496299
2.675-2.7470.367480.292923971100
2.747-2.8270.344490.262899948100
2.827-2.9180.264490.225940989100
2.918-3.0220.218480.222913961100
3.022-3.1430.315480.213906954100
3.143-3.2850.151510.1839511002100
3.285-3.4580.239460.163892938100
3.458-3.6730.312500.189936986100
3.673-3.9540.191500.182923973100
3.954-4.3480.21470.16900947100
4.348-4.9690.186490.139928977100
4.969-6.2270.164480.17920968100
6.227-19.6940.225510.254925976100
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)
10.7820.2454-0.0440.47770.36181.77050.3214-0.15750.1354-0.25860.0001-0.2803-0.01610.1942-0.24490.42280.07990.08220.33420.06810.54297.2791-11.9273-19.325
21.5764-0.34750.07061.2920.8771-0.7523-0.0188-0.41420.26690.2252-0.0823-0.2203-0.5473-0.2406-0.14621.42810.2621-0.0071.0020.05021.210719.9229-25.8474-43.2071
32.01054.0425-1.40614.81830.05852.3376-0.1098-0.1180.1118-0.0644-0.19550.0950.39930.84760.29050.75940.32240.15311.01620.20850.8187.1653-17.5696-24.5964
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1:68 OR RESID 118:151)A1 - 68
2X-RAY DIFFRACTION1CHAIN A AND (RESID 1:68 OR RESID 118:151)A118 - 151
3X-RAY DIFFRACTION2CHAIN A AND (RESID 69:117)A69 - 117
4X-RAY DIFFRACTION3CHAIN BB1 - 6

+
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