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- PDB-5bq1: Capturing Carbon Dioxide in beta Carbonic Anhydrase -

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Basic information

Entry
Database: PDB / ID: 5bq1
TitleCapturing Carbon Dioxide in beta Carbonic Anhydrase
ComponentsCarbonic anhydrase
KeywordsLYASE / Carbonic Anhydrase / Metalloenzyme
Function / homology
Function and homology information


carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
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
CARBON DIOXIDE / Carbonic anhydrase / Carbonic anhydrase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsAggarwal, M. / Chua, T.K. / Pinard, M.A. / Szebenyi, D.M. / McKenna, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM25154 United States
CitationJournal: Biochemistry / Year: 2015
Title: Carbon Dioxide "Trapped" in a beta-Carbonic Anhydrase.
Authors: Aggarwal, M. / Chua, T.K. / Pinard, M.A. / Szebenyi, D.M. / McKenna, R.
History
DepositionMay 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 4, 2015Group: Database references
Revision 1.2Nov 11, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,8214
Polymers23,6681
Non-polymers1533
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.874, 78.114, 87.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-303-

CO2

21A-403-

HOH

31A-406-

HOH

41A-456-

HOH

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Components

#1: Protein Carbonic anhydrase /


Mass: 23667.893 Da / Num. of mol.: 1 / Fragment: UNP residues 235-442
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: PAMH19_3356 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A0A8RL02, UniProt: Q9HVB9*PLUS, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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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: 2.6 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 295 K / Method: evaporation / pH: 7 / Details: PEG 200, Tris-HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionRedundancy: 14.1 % / Number: 458548 / Rmerge(I) obs: 0.085 / Χ2: 3.76 / D res high: 1.6 Å / D res low: 50 Å / Num. obs: 32600 / % possible obs: 99.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obsChi squaredRedundancy
4.345010.076.78212.4
3.454.3410.0696.26913.9
3.013.4510.0735.914.5
2.743.0110.085.48814.6
2.542.7410.0865.23714.6
2.392.5410.0924.8414.7
2.272.3910.0994.75214.7
2.172.2710.1074.43614.6
2.092.1710.1154.02814.7
2.022.0910.133.714.7
1.952.0210.1453.35114.6
1.91.9510.1652.97114.6
1.851.910.1912.65614.5
1.81.8510.2182.4714.5
1.761.810.2642.32614.5
1.721.7610.2882.22314.5
1.691.7210.3532.00914.4
1.661.6910.4051.76113.2
1.631.6610.4471.6512.1
1.61.6310.4991.56210.9
ReflectionResolution: 1.6→50 Å / Num. obs: 32600 / % possible obs: 99.3 % / Redundancy: 14.1 % / Biso Wilson estimate: 22.86 Å2 / Rmerge(I) obs: 0.085 / Χ2: 3.764 / Net I/av σ(I): 72.784 / Net I/σ(I): 15.7 / Num. measured all: 458548
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.6-1.6310.90.49915851.56298.3
1.63-1.6612.10.44715991.65100
1.66-1.6913.20.40516241.761100
1.69-1.7214.40.35316472.009100
1.72-1.7614.50.28816062.223100
1.76-1.814.50.26416202.326100
1.8-1.8514.50.21816202.47100
1.85-1.914.50.19116232.656100
1.9-1.9514.60.16516432.971100
1.95-2.0214.60.14516193.351100
2.02-2.0914.70.1316413.7100
2.09-2.1714.70.11516274.02899.9
2.17-2.2714.60.10716344.436100
2.27-2.3914.70.09916364.752100
2.39-2.5414.70.09216464.84100
2.54-2.7414.60.08616555.237100
2.74-3.0114.60.0816655.48899.9
3.01-3.4514.50.07316555.999.6
3.45-4.3413.90.06916386.26997.6
4.34-5012.40.0716176.78291.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PDB_EXTRACT3.15data extraction
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→29.166 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1994 1997 6.14 %
Rwork0.1735 30533 -
obs0.1751 32530 99.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.4 Å2 / Biso mean: 32.2949 Å2 / Biso min: 16.68 Å2
Refinement stepCycle: final / Resolution: 1.6→29.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 7 110 1776
Biso mean--32.94 36.03 -
Num. residues----209
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061716
X-RAY DIFFRACTIONf_angle_d0.9982336
X-RAY DIFFRACTIONf_chiral_restr0.04267
X-RAY DIFFRACTIONf_plane_restr0.004302
X-RAY DIFFRACTIONf_dihedral_angle_d13.279621
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.64140.2231430.21392117226099
1.6414-1.68570.20771340.19622002334100
1.6857-1.73530.20551540.187221342288100
1.7353-1.79130.20141440.174521662310100
1.7913-1.85540.17331210.168122072328100
1.8554-1.92960.18721530.175321422295100
1.9296-2.01740.2551400.17522012341100
2.0174-2.12380.22271440.173821802324100
2.1238-2.25680.15351370.174321912328100
2.2568-2.43090.17641500.170321832333100
2.4309-2.67540.1961410.17982213235499
2.6754-3.06220.21281480.18121942342100
3.0622-3.85670.21891420.17362222236499
3.8567-29.17120.18661460.16172183232993
Refinement TLS params.Method: refined / Origin x: -27.4153 Å / Origin y: -2.8653 Å / Origin z: -16.3073 Å
111213212223313233
T0.2101 Å2-0.0159 Å20.0206 Å2-0.2024 Å2-0.0024 Å2--0.2103 Å2
L0.8736 °20.0889 °20.2845 °2-0.2238 °2-0.1024 °2--1.559 °2
S-0.0819 Å °0.1314 Å °-0.0372 Å °-0.1096 Å °0.0177 Å °-0.0317 Å °0.0347 Å °0.1481 Å °-0 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:211 OR RESID 302:302 OR RESID 301:301 OR RESID 401:510 OR RESID 303:303 ) )A3 - 211
2X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:211 OR RESID 302:302 OR RESID 301:301 OR RESID 401:510 OR RESID 303:303 ) )A302
3X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:211 OR RESID 302:302 OR RESID 301:301 OR RESID 401:510 OR RESID 303:303 ) )A301
4X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:211 OR RESID 302:302 OR RESID 301:301 OR RESID 401:510 OR RESID 303:303 ) )A401 - 510
5X-RAY DIFFRACTION1( CHAIN A AND ( RESID 3:211 OR RESID 302:302 OR RESID 301:301 OR RESID 401:510 OR RESID 303:303 ) )A303

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