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- PDB-8q6l: human Carbonic Anhydrase I in complex with 3,4-dihydro-1H-benzo[c... -

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Basic information

Entry
Database: PDB / ID: 8q6l
Titlehuman Carbonic Anhydrase I in complex with 3,4-dihydro-1H-benzo[c][1,2]oxaborinin-1-ol
ComponentsCarbonic anhydrase 1
KeywordsLYASE / Carbonic Anhydrase I / inhibitor / metalloenzyme / Benzoxaborine / boro
Function / homology
Function and homology information


hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen ...hydro-lyase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / extracellular exosome / zinc ion binding / cytosol
Similarity search - Function
Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase
Similarity search - Domain/homology
: / Carbonic anhydrase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsAngeli, A. / Ferraroni, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: human Carbonic Anhydrase I in complex with 3,4-dihydro-1H-benzo[c][1,2]oxaborinin-1-ol
Authors: Angeli, A. / Ferraroni, M.
History
DepositionAug 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Carbonic anhydrase 1
BBB: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,2967
Polymers57,8122
Non-polymers4845
Water4,558253
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-11 kcal/mol
Surface area21450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.350, 71.410, 121.460
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Carbonic anhydrase 1 / Carbonate dehydratase I / Carbonic anhydrase B / CAB / Carbonic anhydrase I / CA-I


Mass: 28906.186 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA1 / Production host: Escherichia coli (E. coli) / References: UniProt: P00915, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-KIX / 1,1-bis(oxidanyl)-3,4-dihydro-2,1$l^{4}-benzoxaborinine / 3,4-dihydro-1H-1l4-benzo[c][1,2]oxaborinine-1,1-diol


Mass: 164.974 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10BO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 28-31% PEG4000, 0.2 M Sodium acetate, 0.1 M Tris pH 8.5-9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 0.9717 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9717 Å / Relative weight: 1
ReflectionResolution: 1.72→50 Å / Num. obs: 58501 / % possible obs: 99.6 % / Redundancy: 12.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.104 / Rrim(I) all: 0.108 / Net I/σ(I): 19.06
Reflection shellResolution: 1.72→1.76 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.172 / Mean I/σ(I) obs: 2.31 / Num. unique obs: 4171 / CC1/2: 0.833 / Rrim(I) all: 1.235 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.948 / SU B: 2.804 / SU ML: 0.087 / Cross valid method: NONE / ESU R: 0.112 / ESU R Free: 0.112
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.23 2976 5.087 %
Rwork0.1897 55525 -
all0.192 --
obs-58501 99.586 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.302 Å2
Baniso -1Baniso -2Baniso -3
1--0.839 Å20 Å20 Å2
2--2.251 Å2-0 Å2
3----1.412 Å2
Refinement stepCycle: LAST / Resolution: 1.72→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4024 0 27 253 4304
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0134193
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173686
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.6415717
X-RAY DIFFRACTIONr_angle_other_deg1.3881.5818626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5595521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.85123.738206
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.52115666
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7581514
X-RAY DIFFRACTIONr_chiral_restr0.0820.2536
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024792
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02854
X-RAY DIFFRACTIONr_nbd_refined0.2020.2759
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.23492
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21995
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.21877
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2194
X-RAY DIFFRACTIONr_metal_ion_refined0.1040.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2550.26
X-RAY DIFFRACTIONr_nbd_other0.20.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1070.213
X-RAY DIFFRACTIONr_mcbond_it1.9712.3362060
X-RAY DIFFRACTIONr_mcbond_other1.9712.3362061
X-RAY DIFFRACTIONr_mcangle_it2.7383.4962574
X-RAY DIFFRACTIONr_mcangle_other2.7383.4962575
X-RAY DIFFRACTIONr_scbond_it2.8352.5962133
X-RAY DIFFRACTIONr_scbond_other2.8342.5962134
X-RAY DIFFRACTIONr_scangle_it4.2583.7733138
X-RAY DIFFRACTIONr_scangle_other4.2583.7743139
X-RAY DIFFRACTIONr_lrange_it5.22927.1464536
X-RAY DIFFRACTIONr_lrange_other5.2327.154533
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.7610.3172100.2863952X-RAY DIFFRACTION97.1976
1.761-1.8090.2892020.2623924X-RAY DIFFRACTION99.1112
1.809-1.8620.2592240.2413837X-RAY DIFFRACTION99.5587
1.862-1.9190.2611810.2233757X-RAY DIFFRACTION99.7467
1.919-1.9820.2811850.2193628X-RAY DIFFRACTION99.7645
1.982-2.0510.2651860.2143529X-RAY DIFFRACTION99.7583
2.051-2.1290.251800.213379X-RAY DIFFRACTION99.9719
2.129-2.2150.2481900.2073272X-RAY DIFFRACTION99.8558
2.215-2.3140.2651760.1933159X-RAY DIFFRACTION99.97
2.314-2.4260.2341500.1913004X-RAY DIFFRACTION100
2.426-2.5570.2391950.192856X-RAY DIFFRACTION99.9672
2.557-2.7120.2031410.1812741X-RAY DIFFRACTION99.9653
2.712-2.8990.2161360.1892553X-RAY DIFFRACTION99.9628
2.899-3.1310.2291280.192409X-RAY DIFFRACTION100
3.131-3.4290.2281160.1922215X-RAY DIFFRACTION100
3.429-3.8320.2291110.1792013X-RAY DIFFRACTION100
3.832-4.4220.191960.1511797X-RAY DIFFRACTION99.9472
4.422-5.4090.198670.1421550X-RAY DIFFRACTION100
5.409-7.620.187590.1571229X-RAY DIFFRACTION99.9224
7.62-500.17430.18721X-RAY DIFFRACTION99.0921

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