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- PDB-6y04: Crystal structure of beta-carbonic anhydrase isoform I (TvaCA1) f... -

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Basic information

Entry
Database: PDB / ID: 6y04
TitleCrystal structure of beta-carbonic anhydrase isoform I (TvaCA1) from the Trichomonas vaginalis protozoan.
ComponentsCarbonic anhydrase
KeywordsLYASE / Druggable Enzyme
Function / homologyCarbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding / Carbonic anhydrase
Function and homology information
Biological speciesTrichomonas vaginalis (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsDi Fiore, A. / De Simone, G.
CitationJournal: J Enzyme Inhib Med Chem / Year: 2020
Title: Biochemical and structural characterisation of a protozoan beta-carbonic anhydrase fromTrichomonas vaginalis.
Authors: Urbanski, L.J. / Di Fiore, A. / Azizi, L. / Hytonen, V.P. / Kuuslahti, M. / Buonanno, M. / Monti, S.M. / Angeli, A. / Zolfaghari Emameh, R. / Supuran, C.T. / De Simone, G. / Parkkila, S.
History
DepositionFeb 6, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase
B: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0334
Polymers39,9022
Non-polymers1312
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8040 Å2
ΔGint-134 kcal/mol
Surface area14700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.300, 77.300, 90.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: _ / Auth seq-ID: 1 - 182 / Label seq-ID: 1 - 182

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Carbonic anhydrase / Carbonate dehydratase


Mass: 19951.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichomonas vaginalis (eukaryote) / Gene: TVAG_005270 / Production host: Escherichia coli (E. coli) / References: UniProt: A2ENQ8, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.08 Å3/Da / Density % sol: 40.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 30% (w/v) polyethylene glycol 4000, 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.5

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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: Jul 8, 2019 / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.48→41.9 Å / Num. obs: 12403 / % possible obs: 99.9 % / Redundancy: 13.5 % / Rmerge(I) obs: 0.152 / Rpim(I) all: 0.042 / Rrim(I) all: 0.158 / Χ2: 1.065 / Net I/σ(I): 7.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.48-2.524.50.5725920.7770.2910.6461.07497.9
2.52-2.576.10.5816150.830.2520.6361.08299.8
2.57-2.628.10.5996080.880.2230.641.083100
2.62-2.679.50.5646110.9140.1910.5961.072100
2.67-2.7310.30.4695950.9520.1520.4931.086100
2.73-2.79110.4446120.9540.1390.4661.092100
2.79-2.8612.10.3956050.960.1180.4131.077100
2.86-2.9412.80.3486090.9750.1010.3631.096100
2.94-3.0313.50.3095950.9850.0870.3211.094100
3.03-3.1214.20.2446340.9890.0670.2531.071100
3.12-3.2415.60.226120.9910.0570.2281.03100
3.24-3.3717.30.196170.9940.0470.1951.063100
3.37-3.5217.30.1446100.9960.0350.1481.088100
3.52-3.717.30.1366120.9970.0330.141.041100
3.7-3.9417.20.1176350.9980.0290.1211.092100
3.94-4.2417.20.1026180.9980.0250.1061.043100
4.24-4.67170.0826280.9980.020.0851.026100
4.67-5.3416.80.0866470.9980.0210.0881.05100
5.34-6.7316.50.1016410.9980.0250.1041.049100
6.73-41.914.90.0827070.9980.0220.0851.06499.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
SCALEPACKdata scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G5C

1g5c


Resolution: 2.48→41.9 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.887 / SU B: 10.216 / SU ML: 0.223 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.345 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 944 8.1 %RANDOM
Rwork0.1981 ---
obs0.2026 10698 94.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.12 Å2 / Biso mean: 25.314 Å2 / Biso min: 5.19 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å2-0 Å20 Å2
2--2.96 Å20 Å2
3----1.6 Å2
Refinement stepCycle: final / Resolution: 2.48→41.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2790 0 2 64 2856
Biso mean--30.98 17.97 -
Num. residues----364
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0122843
X-RAY DIFFRACTIONr_angle_refined_deg1.011.633850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2295362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75624.426122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88415520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1471510
X-RAY DIFFRACTIONr_chiral_restr0.0850.2402
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022070
Refine LS restraints NCS

Ens-ID: 1 / Number: 5554 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.05 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.48→2.544 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 64 -
Rwork0.266 687 -
all-751 -
obs--84.67 %

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