[English] 日本語
Yorodumi
- PDB-8gpp: Acinetobacter baumannii carbonic anhydrase PaaY -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gpp
TitleAcinetobacter baumannii carbonic anhydrase PaaY
ComponentsCarbonic anhydrase
KeywordsCARBOHYDRATE / Acinetobacter baumannii / carbonic anhydrase / trimer
Function / homologyHexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / BICARBONATE ION / Carbonic anhydrase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsWen, Y. / Jiao, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82072237; 31870132 China
CitationJournal: Structure / Year: 2023
Title: Acinetobacter baumannii carbonic anhydrase
Authors: Wen, Y. / Jiao, M.
History
DepositionAug 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Carbonic anhydrase
B: Carbonic anhydrase
C: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,76810
Polymers68,3483
Non-polymers4197
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11440 Å2
ΔGint-168 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.073, 93.123, 56.445
Angle α, β, γ (deg.)90.000, 109.410, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 123 or (resid 124...
21(chain B and (resid 2 through 92 or (resid 93...
31(chain C and (resid 2 through 92 or (resid 93...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTHRTHR(chain A and (resid 2 through 123 or (resid 124...AA2 - 1239 - 130
12LYSLYSLYSLYS(chain A and (resid 2 through 123 or (resid 124...AA124131
13PROPROSERSER(chain A and (resid 2 through 123 or (resid 124...AA2 - 1909 - 197
21PROPROGLYGLY(chain B and (resid 2 through 92 or (resid 93...BB2 - 929 - 99
22LYSLYSLYSLYS(chain B and (resid 2 through 92 or (resid 93...BB93100
23PROPROSERSER(chain B and (resid 2 through 92 or (resid 93...BB2 - 1909 - 197
31PROPROGLYGLY(chain C and (resid 2 through 92 or (resid 93...CC2 - 929 - 99
32LYSLYSLYSLYS(chain C and (resid 2 through 92 or (resid 93...CC93100
33HISHISSERSER(chain C and (resid 2 through 92 or (resid 93...CC1 - 1908 - 197

-
Components

#1: Protein Carbonic anhydrase / PaaY


Mass: 22782.805 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: paaY, ATCC19606_22550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6F8THQ5
#2: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.59 Å3/Da / Density % sol: 33.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M PCTP buffer (propionic acid, cacodylate, bis-tris propane) pH = 8.0, 25% (w/v) PEG 1500

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.09→48.17 Å / Num. obs: 28739 / % possible obs: 97.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 38.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1344 / Net I/σ(I): 10.14
Reflection shellResolution: 2.09→2.17 Å / Rmerge(I) obs: 1.439 / Num. unique obs: 2509 / CC1/2: 0.511

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GPM

8gpm


Resolution: 2.09→48.17 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.16 / Phase error: 30.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1998 6.95 %
Rwork0.1968 51914 -
obs0.2008 28739 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.27 Å2 / Biso mean: 49.2061 Å2 / Biso min: 26.25 Å2
Refinement stepCycle: final / Resolution: 2.09→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 19 114 4429
Biso mean--60.54 49.81 -
Num. residues----569
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1140X-RAY DIFFRACTION1.117TORSIONAL
12B1140X-RAY DIFFRACTION1.117TORSIONAL
13C1140X-RAY DIFFRACTION1.117TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.120.4176960.38521335143171
2.12-2.140.38021180.36941609172784
2.15-2.170.31231280.32361705183389
2.17-2.20.34831400.3271852199296
2.2-2.230.39661430.30751908205199
2.23-2.270.34561430.30241906204999
2.27-2.30.29761430.29231909205299
2.3-2.340.3391380.26491902204099
2.34-2.380.3551410.26561910205199
2.38-2.420.34371410.26111896203798
2.42-2.470.30781460.25161882202898
2.47-2.520.30081420.24711858200098
2.52-2.580.33921400.24071877201796
2.58-2.640.26341400.21821850199099
2.64-2.70.26521430.22631922206599
2.7-2.780.29451430.20221908205199
2.78-2.860.22121440.20891913205799
2.86-2.950.22861450.20011908205399
2.95-3.050.3071380.21321846198498
3.05-3.180.28511420.20651862200496
3.18-3.320.25931410.192919462087100
3.32-3.50.27431440.193519002044100
3.5-3.720.261370.17721896203399
3.72-40.2431420.16621913205598
4-4.410.18331380.13981875201398
4.41-5.040.20151400.14171873201398
5.04-6.350.21111400.16571885202597
6.35-48.170.18011430.14541868201198
Refinement TLS params.Method: refined / Origin x: 8.6556 Å / Origin y: 0.7655 Å / Origin z: 14.6631 Å
111213212223313233
T0.2526 Å20.0131 Å20.0006 Å2-0.2589 Å2-0.0069 Å2--0.2231 Å2
L1.2035 °20.0655 °2-0.1279 °2-2.8595 °2-0.5779 °2--1.0433 °2
S-0.0697 Å °-0.0865 Å °-0.0258 Å °0.1176 Å °0.11 Å °-0.0958 Å °-0.0618 Å °-0.0729 Å °-0.0393 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 190
2X-RAY DIFFRACTION1allA201
3X-RAY DIFFRACTION1allB2 - 190
4X-RAY DIFFRACTION1allB201
5X-RAY DIFFRACTION1allC1 - 201
6X-RAY DIFFRACTION1allD1 - 3
7X-RAY DIFFRACTION1allE1
8X-RAY DIFFRACTION1allS1 - 116

+
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