[English] 日本語
Yorodumi
- PDB-7zw9: Crystal structure of a gamma-carbonic anhydrase from the pathogen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zw9
TitleCrystal structure of a gamma-carbonic anhydrase from the pathogenic bacterium Burkholderia pseudomallei
ComponentsBacterial transferase hexapeptide family protein
KeywordsLYASE / Bacterial target
Function / homology: / : / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / transferase activity / BETA-MERCAPTOETHANOL / Bacterial transferase hexapeptide family protein
Function and homology information
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsDi Fiore, A. / De Simone, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Comput Struct Biotechnol J / Year: 2022
Title: Biochemical, structural, and computational studies of a gamma-carbonic anhydrase from the pathogenic bacterium Burkholderia pseudomallei.
Authors: Di Fiore, A. / De Luca, V. / Langella, E. / Nocentini, A. / Buonanno, M. / Maria Monti, S. / Supuran, C.T. / Capasso, C. / De Simone, G.
History
DepositionMay 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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: Bacterial transferase hexapeptide family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6213
Polymers22,4781
Non-polymers1442
Water1,09961
1
A: Bacterial transferase hexapeptide family protein
hetero molecules

A: Bacterial transferase hexapeptide family protein
hetero molecules

A: Bacterial transferase hexapeptide family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,8639
Polymers67,4333
Non-polymers4316
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area6980 Å2
ΔGint-142 kcal/mol
Surface area18260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.130, 90.130, 48.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

21A-359-

HOH

31A-361-

HOH

-
Components

#1: Protein Bacterial transferase hexapeptide family protein / Gamma carbonic anhydrase family protein / Hexapeptide repeat-containing transferase


Mass: 22477.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria)
Gene: yrdA, BOC38_15155, CXQ84_07800, DF122_29500, DP49_2200, ERS012318_04959, SAMEA1968934_03882, X994_171
Production host: Escherichia coli (E. coli) / References: UniProt: A0A069B6L3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% (w/v) Polyethylene glycol 3350, 0.15 M DL-malic acid pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Feb 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 13267 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.043 / Rrim(I) all: 0.133 / Χ2: 1.016 / Net I/σ(I): 6.7 / Num. measured all: 127556
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.145.50.636580.8540.2920.6960.948100
2.14-2.186.30.6366440.8810.2750.6941.002100
2.18-2.226.80.4746640.9510.1960.5141.01100
2.22-2.267.40.4556520.9510.1810.490.959100
2.26-2.3180.4266770.9590.160.4560.991100
2.31-2.378.50.4076480.9650.1490.4341100
2.37-2.429.10.3686570.9860.1290.390.997100
2.42-2.499.70.3736620.990.1260.3940.995100
2.49-2.5610.80.3156540.9890.10.3310.996100
2.56-2.6510.90.2966600.9950.0940.3111.002100
2.65-2.7410.90.2636600.9920.0830.2761.032100
2.74-2.85110.2336670.9920.0740.2451.065100
2.85-2.98110.1746450.9960.0550.1831.048100
2.98-3.14110.1236680.9990.0390.1291.007100
3.14-3.33110.1076700.9990.0340.1121.021100
3.33-3.59110.0856590.9990.0270.0891.01100
3.59-3.95110.0716710.9990.0230.0741.089100
3.95-4.5210.90.0616750.9990.020.0641.025100
4.52-5.710.90.04967710.0160.0521.012100
5.7-5010.30.04669910.0160.0481.01799.3

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4N27

4n27


Resolution: 2.1→30.4 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2314 1005 7.6 %
Rwork0.1967 11556 -
obs-12561 94.6 %
Solvent computationBsol: 59.3305 Å2
Displacement parametersBiso max: 55 Å2 / Biso mean: 22.6268 Å2 / Biso min: 7.68 Å2
Baniso -1Baniso -2Baniso -3
1--2.218 Å2-0 Å2-0 Å2
2---2.218 Å2-0 Å2
3---4.435 Å2
Refinement stepCycle: final / Resolution: 2.1→30.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1279 0 5 61 1345
Biso mean--29.55 29.71 -
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.534
X-RAY DIFFRACTIONc_mcbond_it1.2341.5
X-RAY DIFFRACTIONc_scbond_it2.3772
X-RAY DIFFRACTIONc_mcangle_it1.8172
X-RAY DIFFRACTIONc_scangle_it3.3172.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.180.2903880.26391023111185.1
2.18-2.260.2853960.21271078117490
2.26-2.370.23841020.20821153125593.7
2.37-2.490.2352900.20091128121893
2.49-2.650.2398940.19981158125294.9
2.65-2.850.29061090.21241163127295.2
2.85-3.140.2097950.19761180127597.6
3.14-3.590.2216990.19721216131598.6
3.59-4.520.2068940.17041232132698.6
4.52-30.40.20971380.18781225136399.1
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6bme_mod.param

+
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