[English] 日本語
Yorodumi
- PDB-7a03: The Structure of CHT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7a03
TitleThe Structure of CHT
ComponentsM32 carboxypeptidase
KeywordsHYDROLASE / Carboxypeptidase / Metalloenzyme
Function / homologyCITRIC ACID / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesChitinophagaceae bacterium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.39 Å
AuthorsFernandes, G. / Machado, E. / Pereira, M. / Brear, P. / Lemos, E.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Coordination for the Improvement of Higher Education Personnel001 Brazil
CitationJournal: To Be Published
Title: Exploring the genome of Chitinophaga (CB10) for metalocarboxipeptidase activity
Authors: Fernandes, G. / Machado, E. / Pereira, M. / Brear, P. / Lemos, E.
History
DepositionAug 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2021Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: M32 carboxypeptidase
B: M32 carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)115,94911
Polymers114,9062
Non-polymers1,0439
Water10,521584
1
A: M32 carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,0286
Polymers57,4531
Non-polymers5755
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: M32 carboxypeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,9225
Polymers57,4531
Non-polymers4684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.095, 110.266, 113.871
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein M32 carboxypeptidase


Mass: 57453.109 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chitinophagaceae bacterium (bacteria)
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.64 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.1 M Na3 Cit pH 5 20% w/v PEG 6K

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Aug 7, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.39→71.133 Å / Num. obs: 234729 / % possible obs: 100 % / Redundancy: 10 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.027 / Rrim(I) all: 0.086 / Net I/σ(I): 13.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.39-1.43101.791.1171980.5760.5881.886100
6.22-71.139.70.03128920.9980.010.03299.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.32data scaling
PHASERphasing
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Unpublished

Resolution: 1.39→71.133 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2655 11365 5.04 %
Rwork0.2453 214329 -
obs0.2463 225694 96.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.26 Å2 / Biso mean: 22.1172 Å2 / Biso min: 9.51 Å2
Refinement stepCycle: final / Resolution: 1.39→71.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8035 0 52 584 8671
Biso mean--31.19 27.21 -
Num. residues----987
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.39-1.40570.42343680.3697717498
1.4057-1.42220.34873710.3734717898
1.4222-1.43960.43832860.5017606082
1.4396-1.45780.42463830.4211720497
1.4578-1.4770.49363770.4575723298
1.477-1.49720.45153040.4649596081
1.4972-1.51860.40284000.3457718497
1.5186-1.54130.41753960.4001717198
1.5413-1.56540.3253780.2885733199
1.5654-1.5910.28794180.269731899
1.591-1.61850.26314010.26657357100
1.6185-1.64790.29673870.26027319100
1.6479-1.67960.26553810.24267378100
1.6796-1.71390.2724130.2405731799
1.7139-1.75120.2674100.23277377100
1.7512-1.79190.24674150.21947312100
1.7919-1.83670.22854090.20677417100
1.8367-1.88640.26764360.2295724799
1.8864-1.94190.63542520.6085471364
1.9419-2.00460.26143720.2425730398
2.0046-2.07620.26453770.2299735799
2.0762-2.15930.23453730.1996742699
2.1593-2.25760.43313290.3931675991
2.2576-2.37670.28033820.2396685692
2.3767-2.52560.21493910.1957467100
2.5256-2.72060.23243700.19787499100
2.7206-2.99440.20913950.19477501100
2.9944-3.42770.21664120.20117520100
3.4277-4.31840.20664020.1866749699
4.3184-71.1330.15073770.16237896100
Refinement TLS params.Method: refined / Origin x: -7.6768 Å / Origin y: -3.7448 Å / Origin z: 29.3184 Å
111213212223313233
T0.0768 Å2-0.0035 Å2-0.008 Å2-0.1764 Å20.0147 Å2--0.1077 Å2
L0.4196 °20.031 °2-0.06 °2-0.2027 °2-0.1076 °2--0.2342 °2
S0.0031 Å °0.0622 Å °0.023 Å °0.0059 Å °-0.0019 Å °-0.0006 Å °0.0042 Å °-0.005 Å °-0.0029 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 500
2X-RAY DIFFRACTION1allB6 - 499
3X-RAY DIFFRACTION1allD1 - 7
4X-RAY DIFFRACTION1allE2 - 616
5X-RAY DIFFRACTION1allC1
6X-RAY DIFFRACTION1allF1 - 2

+
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