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- PDB-9ebz: Escherichia coli Carbonic Anhydrase 2 in Space Group C222(1) -

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Basic information

Entry
Database: PDB / ID: 9ebz
TitleEscherichia coli Carbonic Anhydrase 2 in Space Group C222(1)
ComponentsCarbonic anhydrase
KeywordsLYASE / Zinc-dependent metalloprotein
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 / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase
Similarity search - Domain/homology
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsRankin, M.R. / Smith, J.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK042303 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)F31CA265082 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2025
Title: Serendipitous high-resolution structure of Escherichia coli carbonic anhydrase 2.
Authors: Rankin, M.R. / Smith, J.L.
History
DepositionNov 13, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase
B: Carbonic anhydrase
C: Carbonic anhydrase
D: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,7858
Polymers100,5234
Non-polymers2624
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15670 Å2
ΔGint-85 kcal/mol
Surface area32750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.227, 119.145, 161.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
Carbonic anhydrase / Carbonate dehydratase


Mass: 25130.779 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: Native / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A140NBR3, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 200 mM ammonium tartrate dibasic, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.66→47.89 Å / Num. obs: 31559 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 63.72 Å2 / CC1/2: 0.994 / Net I/σ(I): 6
Reflection shellResolution: 2.66→2.73 Å / Num. unique obs: 3099 / CC1/2: 0.584

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→47.89 Å / SU ML: 0.515 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 38.7874
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2873 2005 6.37 %
Rwork0.2606 29482 -
obs0.2624 31487 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 82.16 Å2
Refinement stepCycle: LAST / Resolution: 2.66→47.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6824 0 4 3 6831
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00396972
X-RAY DIFFRACTIONf_angle_d0.64959459
X-RAY DIFFRACTIONf_chiral_restr0.04471055
X-RAY DIFFRACTIONf_plane_restr0.00561216
X-RAY DIFFRACTIONf_dihedral_angle_d12.32742545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.66-2.730.49841440.47552077X-RAY DIFFRACTION99.82
2.73-2.80.48621400.44362042X-RAY DIFFRACTION99.23
2.8-2.880.46871470.41712098X-RAY DIFFRACTION99.69
2.88-2.980.43311370.38742088X-RAY DIFFRACTION99.64
2.98-3.080.38181480.36262055X-RAY DIFFRACTION99.64
3.08-3.210.3441270.31842106X-RAY DIFFRACTION99.64
3.21-3.350.31471520.29672093X-RAY DIFFRACTION99.47
3.35-3.530.34451430.28282090X-RAY DIFFRACTION99.64
3.53-3.750.32341390.27442100X-RAY DIFFRACTION99.29
3.75-4.040.26741360.26842102X-RAY DIFFRACTION99.6
4.04-4.440.23611470.23542099X-RAY DIFFRACTION99.87
4.44-5.090.27071410.20742143X-RAY DIFFRACTION99.83
5.09-6.410.27231500.23442158X-RAY DIFFRACTION99.87
6.41-47.890.18891540.18242231X-RAY DIFFRACTION99.62

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