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- PDB-7bf0: Zn-bound domain 3 of CDCA1 in complex with carbon dioxide -

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Basic information

Entry
Database: PDB / ID: 7bf0
TitleZn-bound domain 3 of CDCA1 in complex with carbon dioxide
ComponentsCadmium-specific carbonic anhydrase
KeywordsLYASE / CARBON DIOXIDE / CARBONIC ANHYDRASE / ZINC-BOUND / MARINE DIATOM
Function / homologyCadmium carbonic anhydrase repeat / Cadmium carbonic anhydrase repeat / metal ion binding / CARBON DIOXIDE / Cadmium-specific carbonic anhydrase
Function and homology information
Biological speciesThalassiosira weissflogii (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsAlterio, V. / De Simone, G.
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: Zeta-carbonic anhydrases show CS 2 hydrolase activity: A new metabolic carbon acquisition pathway in diatoms?
Authors: Alterio, V. / Langella, E. / Buonanno, M. / Esposito, D. / Nocentini, A. / Berrino, E. / Bua, S. / Polentarutti, M. / Supuran, C.T. / Monti, S.M. / De Simone, G.
History
DepositionDec 30, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 14, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Cadmium-specific carbonic anhydrase
B: Cadmium-specific carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9077
Polymers49,6532
Non-polymers2545
Water3,081171
1
A: Cadmium-specific carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9714
Polymers24,8261
Non-polymers1453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cadmium-specific carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9363
Polymers24,8261
Non-polymers1092
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.576, 62.712, 75.018
Angle α, β, γ (deg.)90.000, 119.780, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Cadmium-specific carbonic anhydrase / (CDCA1-R3)


Mass: 24826.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: MARINE DIATOM / Source: (gene. exp.) Thalassiosira weissflogii (Diatom) / Gene: cdca1 / Plasmid: PET15B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q50EL4
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CO2 / CARBON DIOXIDE


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.9
Details: 28% (w/v) PEG2000, 20 mM lithium sulfate, 100 mM sodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.999995 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999995 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 61450 / % possible obs: 97 % / Redundancy: 11.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.019 / Rrim(I) all: 0.068 / Χ2: 1.039 / Net I/av σ(I): 35.8 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.6-1.637.10.4433.924490.9490.1620.4741.0178
1.63-1.667.60.4234.225820.9480.1510.4510.97982.3
1.66-1.698.10.3844.628330.960.1320.4080.96889.8
1.69-1.729.40.3745.329870.9690.120.3941.06795.1
1.72-1.7610.30.326730850.9780.1020.3431.08698
1.76-1.8110.38.331490.9830.0920.3141.07799.8
1.8-1.8511.60.2741031540.9880.0830.2871.0799.9
1.85-1.911.30.2511.431480.9910.0770.2621.09899.9
1.9-1.9512.40.2161431580.9930.0630.2251.07299.9
1.95-2.0213.10.17617.931290.9950.050.1831.0999.7
2.02-2.0912.80.14820.331840.9960.0430.1541.06299.9
2.09-2.1711.90.12322.731510.9970.0370.1281.07599.8
2.17-2.2713.20.10427.431470.9980.030.1091.02799.7
2.27-2.3913.30.09130.131400.9980.0260.0950.98899.8
2.39-2.5412.60.07832.431680.9980.0230.0810.98399.7
2.54-2.7412.40.06638.731500.9990.0190.0691.07599.5
2.74-3.0113.10.0564331810.9990.0160.0590.96999.7
3.01-3.4512.40.04944.831860.9990.0140.0510.974100
3.45-4.3412.80.0435431950.9990.0120.0451.075100
4.34-5012.60.04150.632740.9990.0120.0430.997100

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UK8

3uk8


Resolution: 1.6→50 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 960 1.5 %Random selection
Rwork0.2147 57168 --
obs-58128 91.4 %-
Displacement parametersBiso max: 60.81 Å2 / Biso mean: 26.3624 Å2 / Biso min: 12.08 Å2
Baniso -1Baniso -2Baniso -3
1-13.341 Å2-0 Å27.237 Å2
2---5.442 Å20 Å2
3----7.899 Å2
Refinement stepCycle: final / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3183 0 9 171 3363
Biso mean--28.88 30.46 -
Num. residues----423
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.535
X-RAY DIFFRACTIONc_mcbond_it1.1971.5
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_mcangle_it1.7212
X-RAY DIFFRACTIONc_scangle_it2.7042.5
LS refinement shell
Resolution (Å)Refine-ID
1.6-1.66X-RAY DIFFRACTION
1.66-1.72X-RAY DIFFRACTION
1.72-1.8X-RAY DIFFRACTION
1.8-1.9X-RAY DIFFRACTION
1.9-2.02X-RAY DIFFRACTION
2.02-2.17X-RAY DIFFRACTION
2.17-2.39X-RAY DIFFRACTION
2.39-2.74X-RAY DIFFRACTION
2.74-3.45X-RAY DIFFRACTION
3.45-50X-RAY DIFFRACTION

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