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- PDB-9eat: High-Resolution Structure of Escherichia coli Carbonic Anhydrase ... -

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Basic information

Entry
Database: PDB / ID: 9eat
TitleHigh-Resolution Structure of Escherichia coli Carbonic Anhydrase 2 in Space Group P4(2)2(1)2
ComponentsCarbonic anhydrase 2
KeywordsLYASE / Zinc-dependent metalloenzyme
Function / homology
Function and homology information


carbon utilization / carbonic anhydrase / carbonate dehydratase activity / protein homotetramerization / zinc ion binding / identical protein binding / cytosol
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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesEscherichia coli BL21 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.43 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 11, 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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1962
Polymers25,1311
Non-polymers651
Water4,216234
1
A: Carbonic anhydrase 2
hetero molecules

A: Carbonic anhydrase 2
hetero molecules

A: Carbonic anhydrase 2
hetero molecules

A: Carbonic anhydrase 2
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_665-x+1,-y+1,z1
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_666-y+1,-x+1,-z+11
Buried area15550 Å2
ΔGint-94 kcal/mol
Surface area33050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.524, 67.524, 85.076
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Space group name HallP4n2n
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/2
#3: y+1/2,-x+1/2,z+1/2
#4: x+1/2,-y+1/2,-z+1/2
#5: -x+1/2,y+1/2,-z+1/2
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
Components on special symmetry positions
IDModelComponents
11A-486-

HOH

21A-553-

HOH

31A-614-

HOH

41A-623-

HOH

51A-626-

HOH

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase 2


Mass: 25130.779 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Native / Source: (natural) Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61517, carbonic anhydrase
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 1.93 Å3/Da / Density % sol: 36.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100 mM HEPES pH 7.5, 200 mM lithium sulfate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 21, 2022
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.43→47.77 Å / Num. obs: 69116 / % possible obs: 99.48 % / Redundancy: 6.41 % / Biso Wilson estimate: 14.77 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.108 / Net I/σ(I): 13.1
Reflection shellResolution: 1.43→1.48 Å / Redundancy: 3.58 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 6625 / CC1/2: 0.415 / Rrim(I) all: 1.106 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.43→47.75 Å / SU ML: 0.152 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 16.2324
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1674 3740 5.41 %
Rwork0.1562 65375 -
obs0.1568 69115 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.01 Å2
Refinement stepCycle: LAST / Resolution: 1.43→47.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1698 0 1 234 1933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00881757
X-RAY DIFFRACTIONf_angle_d1.04162391
X-RAY DIFFRACTIONf_chiral_restr0.0778269
X-RAY DIFFRACTIONf_plane_restr0.0067307
X-RAY DIFFRACTIONf_dihedral_angle_d13.3979648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.450.35041330.3242294X-RAY DIFFRACTION93.85
1.45-1.470.30411360.30822343X-RAY DIFFRACTION95.68
1.47-1.490.29771350.28162338X-RAY DIFFRACTION97.63
1.49-1.510.24291330.25212429X-RAY DIFFRACTION99.03
1.51-1.530.18131390.22162397X-RAY DIFFRACTION99.69
1.53-1.550.21871350.18542452X-RAY DIFFRACTION100
1.55-1.580.19151410.17882430X-RAY DIFFRACTION100
1.58-1.610.17141420.17162447X-RAY DIFFRACTION100
1.61-1.640.18061430.16462407X-RAY DIFFRACTION100
1.64-1.670.18011390.15772429X-RAY DIFFRACTION100
1.67-1.70.18871390.15842454X-RAY DIFFRACTION100
1.7-1.740.21651340.15822444X-RAY DIFFRACTION100
1.74-1.780.16981430.15212431X-RAY DIFFRACTION100
1.78-1.820.15481370.1622444X-RAY DIFFRACTION100
1.82-1.870.18751400.1682427X-RAY DIFFRACTION100
1.87-1.930.15731430.14722437X-RAY DIFFRACTION100
1.93-1.990.21021340.14262445X-RAY DIFFRACTION100
1.99-2.060.19241410.14622404X-RAY DIFFRACTION100
2.06-2.140.15631390.14632419X-RAY DIFFRACTION100
2.14-2.240.17061390.13742465X-RAY DIFFRACTION100
2.24-2.360.14621350.13742424X-RAY DIFFRACTION100
2.36-2.510.16091400.14282458X-RAY DIFFRACTION100
2.51-2.70.15861420.14822418X-RAY DIFFRACTION100
2.7-2.970.15011400.15132429X-RAY DIFFRACTION100
2.98-3.40.12741440.14272432X-RAY DIFFRACTION100
3.4-4.290.1431390.13792427X-RAY DIFFRACTION100
4.29-47.750.16021350.15222451X-RAY DIFFRACTION99.96

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