[English] 日本語
Yorodumi
- PDB-4znz: Crystal structure of Escherichia coli carbonic anhydrase (YadF) i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4znz
TitleCrystal structure of Escherichia coli carbonic anhydrase (YadF) in complex with Zn - artifact of purification
ComponentsCarbonic anhydrase
KeywordsLYASE / carbonic anhydrase / YadF / crystallization artifact / zinc binding
Function / homology
Function and homology information


carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Prokaryotic-type carbonic anhydrases signature 1. / Prokaryotic-type carbonic anhydrases signature 2. / Carbonic anhydrase, prokaryotic-like, conserved site / Beta-carbonic Anhydrase; Chain A / Carbonic anhydrase / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Carbonic anhydrase / Carbonic anhydrase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsGasiorowska, O.A. / Niedzialkowska, E. / Porebski, P.J. / Handing, K.B. / Shabalin, I.G. / Cymborowski, M.T. / Minor, W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54-GM094662 United States
CitationJournal: Protein Sci. / Year: 2016
Title: Protein purification and crystallization artifacts: The tale usually not told.
Authors: Niedzialkowska, E. / Gasiorowska, O. / Handing, K.B. / Majorek, K.A. / Porebski, P.J. / Shabalin, I.G. / Zasadzinska, E. / Cymborowski, M. / Minor, W.
History
DepositionMay 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 1.4Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1962
Polymers25,1311
Non-polymers651
Water46826
1
A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7858
Polymers100,5234
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area15130 Å2
ΔGint-92 kcal/mol
Surface area32600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.909, 67.909, 84.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212

-
Components

#1: Protein Carbonic anhydrase /


Mass: 25130.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: BL21-CodonPlus(DE3)-RIL
References: UniProt: C6EAT1, UniProt: A0A140NBR3*PLUS, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 1.95 Å3/Da / Density % sol: 36.86 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.3 ul of 7.4 mg/ml protein in 50 mM TRIS pH 7.9, 200 mM NaCl and 0.5 mM TCEP were mixed with the 0.3 ul of SaltRx condition #96 (60% v/v Tacsimate pH 7.0 and 0.1 M BIS-TRIS propane pH 7.0) ...Details: 0.3 ul of 7.4 mg/ml protein in 50 mM TRIS pH 7.9, 200 mM NaCl and 0.5 mM TCEP were mixed with the 0.3 ul of SaltRx condition #96 (60% v/v Tacsimate pH 7.0 and 0.1 M BIS-TRIS propane pH 7.0) and equilibrated against SaltRx condition #96 solution in 96 Well 3 drop Crystallization Plate (Swissci)
PH range: 7.0 - 7.9

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.27822 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 20, 2013 / Details: Bimorph K-B pair
RadiationMonochromator: Kohzu / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27822 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 5907 / Num. obs: 5527 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 58.2 Å2 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.045 / Rrim(I) all: 0.13 / Rsym value: 0.122 / Χ2: 1.069 / Net I/av σ(I): 18.875 / Net I/σ(I): 6.5 / Num. measured all: 44824
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.758.10.9261.82760.7520.3380.9880.64495.8
2.75-2.88.10.7412750.8470.270.790.68496.2
2.8-2.858.20.7372820.7890.2660.7850.73395.9
2.85-2.918.30.6182620.8110.2240.6590.69996
2.91-2.978.10.5742720.8810.210.6120.72295.4
2.97-3.048.10.5062790.8920.1830.540.80194.9
3.04-3.128.20.4222720.9450.1540.4510.77896.1
3.12-3.28.20.3422760.9620.1240.3650.82994.8
3.2-3.38.20.2772680.9670.1010.2950.86694.4
3.3-3.48.10.2162820.9730.0790.230.92994
3.4-3.528.20.1762580.9940.0640.1880.9795.2
3.52-3.668.30.1382720.9920.0510.1471.09693.5
3.66-3.838.20.1212750.9930.0440.1291.15994.2
3.83-4.038.10.1182840.9930.0430.1261.36693.7
4.03-4.298.20.0952690.9960.0350.1011.33592.1
4.29-4.628.20.0752740.9950.0280.081.54592.9
4.62-5.088.10.0612780.9970.0230.0651.63991.7
5.08-5.818.10.0652830.9980.0230.0691.38691.6
5.81-7.327.90.0582810.9990.0210.0621.48690.1
7.32-507.30.0393090.9980.0150.0421.69486.6

-
Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
HKL-3000phasing
MLPHAREphasing
SHELXphasing
HKL-3000data scaling
HKL-3000data reduction
BLU-MAXdata collection
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.906 / WRfactor Rfree: 0.2318 / WRfactor Rwork: 0.1348 / FOM work R set: 0.8745 / SU B: 11.706 / SU ML: 0.237 / SU Rfree: 0.4107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.411 / SU Rfree Cruickshank DPI: 0.4061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2575 255 4.6 %RANDOM
Rwork0.1488 ---
obs0.1534 5247 93.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.18 Å2 / Biso mean: 53.775 Å2 / Biso min: 29.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å2-0 Å2-0 Å2
2--0.68 Å2-0 Å2
3----1.35 Å2
Refinement stepCycle: final / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1674 0 1 26 1701
Biso mean--42.81 46.16 -
Num. residues----215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191710
X-RAY DIFFRACTIONr_bond_other_d0.0030.021619
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9362326
X-RAY DIFFRACTIONr_angle_other_deg0.99833695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8885214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.18124.05179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.99215282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7611511
X-RAY DIFFRACTIONr_chiral_restr0.0790.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021956
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02405
X-RAY DIFFRACTIONr_mcbond_it4.1655.374859
X-RAY DIFFRACTIONr_mcbond_other4.1295.37858
X-RAY DIFFRACTIONr_mcangle_it6.4048.0541072
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 13 -
Rwork0.185 388 -
all-401 -
obs--96.16 %

+
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