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- PDB-7bez: Zinc bound domain 3 of carbonic anhydrase from marine diatom Thal... -

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Basic information

Entry
Database: PDB / ID: 7bez
TitleZinc bound domain 3 of carbonic anhydrase from marine diatom Thalassiosira weissflogii
ComponentsCadmium-specific carbonic anhydrase
KeywordsLYASE / MARINE DIATOM / CARBONIC ANHYDRASE / ZINC-BOUND
Function / homologyCadmium carbonic anhydrase repeat / Cadmium carbonic anhydrase repeat / metal ion binding / Cadmium-specific carbonic anhydrase
Function and homology information
Biological speciesThalassiosira weissflogii (Diatom)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.981 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
DepositionJan 6, 2021Deposition 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

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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)49,7844
Polymers49,6532
Non-polymers1312
Water2,738152
1
A: Cadmium-specific carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8922
Polymers24,8261
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cadmium-specific carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8922
Polymers24,8261
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)117.754, 62.511, 75.397
Angle α, β, γ (deg.)90.000, 120.060, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.63 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 27% (w/v) PEG3350, 20 mM sodium dihydrogen phosphate, 100 mM HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 31341 / % possible obs: 95.2 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.043 / Rrim(I) all: 0.103 / Χ2: 1.031 / Net I/av σ(I): 13.3 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.98-2.022.70.4542.112570.7940.3110.5550.93775.7
2.02-2.062.80.4042.412880.8450.2730.4920.8881.8
2.06-2.12.80.3412.913960.8860.2270.4130.90283.1
2.1-2.142.90.352.914000.9230.230.4220.90786.4
2.14-2.1930.2754.314390.90.1770.3291.13188.8
2.19-2.243.10.2943.815440.9350.1880.3510.96592.8
2.24-2.33.20.2744.415730.9310.1730.3260.99596.4
2.3-2.363.50.2555.216110.9470.1560.30.98698.6
2.36-2.433.70.2426.116240.9560.1430.2831.04599.6
2.43-2.513.90.221716540.9710.1270.2561.061100
2.51-2.64.20.217.716440.9690.1160.241.082100
2.6-2.74.70.2038.416440.9780.1040.2291.098100
2.7-2.825.10.1818.216220.980.0880.2021.116100
2.82-2.975.20.13711.616380.990.0660.1531.04100
2.97-3.165.40.12213.716830.9910.0570.1351.098100
3.16-3.45.80.09916.516290.9930.0440.1081.062100
3.4-3.746.40.08717.916650.9950.0370.0951.004100
3.74-4.297.90.07226.816500.9970.0270.0771.046100
4.29-5.48.20.05931.616790.9980.0220.0631.042100
5.4-507.90.04935.517010.9980.0190.0530.95599.7

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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: 1.981→33.235 Å / Cross valid method: FREE R-VALUE / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.243 950 2.9 %Random
Rwork0.2085 27820 --
obs-28770 86.9 %-
Displacement parametersBiso max: 59.64 Å2 / Biso mean: 28.1 Å2 / Biso min: 13.17 Å2
Baniso -1Baniso -2Baniso -3
1-18.69 Å2-0 Å29.001 Å2
2---9.123 Å20 Å2
3----9.567 Å2
Refinement stepCycle: final / Resolution: 1.981→33.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3188 0 2 152 3342
Biso mean--24.33 29.77 -
Num. residues----424
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_d1.491
X-RAY DIFFRACTIONc_mcbond_it1.2041.5
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_mcangle_it1.7952
X-RAY DIFFRACTIONc_scangle_it2.8272.5
LS refinement shell
Resolution (Å)Refine-ID
1.981-2.05X-RAY DIFFRACTION
2.05-2.13X-RAY DIFFRACTION
2.13-2.23X-RAY DIFFRACTION
2.23-2.35X-RAY DIFFRACTION
2.35-2.5X-RAY DIFFRACTION
2.5-2.69X-RAY DIFFRACTION
2.69-2.96X-RAY DIFFRACTION
2.96-3.39X-RAY DIFFRACTION
3.39-4.27X-RAY DIFFRACTION
4.27-33.235X-RAY DIFFRACTION

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