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Basic information

Entry
Database: PDB / ID: 7cxw
TitleStructural insights into novel mechanisms of inhibition of the major b-carbonic anhydrase CafB from the pathogenic fungus Aspergillus fumigatus (C116 flipped form)
ComponentsCarbonic anhydrase
KeywordsLYASE / b-class carbonic anhydrase / Zinc metalloenzyme / CafB / Aspergillus fumigatus / oxidative inhibition / zinc-free inactivation
Function / homology
Function and homology information


cellular response to carbon dioxide / carbon utilization / carbonic anhydrase / carbonate dehydratase activity / cellular response to oxidative stress / zinc ion binding / cytoplasm
Similarity search - Function
Prokaryotic-type carbonic anhydrases signature 1. / Carbonic anhydrase, prokaryotic-like, conserved site / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase
Similarity search - Domain/homology
ACETATE ION / Carbonic anhydrase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJin, M.S. / Kim, S. / Yeon, J. / Sung, J. / Kim, N.J. / Hong, S.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2017M3A9F6029753 Korea, Republic Of
National Research Foundation (NRF, Korea)NRF-2019M3E5D6063908 Korea, Republic Of
CitationJournal: J.Struct.Biol. / Year: 2021
Title: Structural insights into novel mechanisms of inhibition of the major beta-carbonic anhydrase CafB from the pathogenic fungus Aspergillus fumigatus.
Authors: Kim, S. / Yeon, J. / Sung, J. / Kim, N.J. / Hong, S. / Jin, M.S.
History
DepositionSep 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)52,2994
Polymers52,1812
Non-polymers1182
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-41 kcal/mol
Surface area19120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.812, 118.812, 68.074
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11B-450-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ALA / End label comp-ID: ALA / Refine code: _ / Auth seq-ID: 10 - 225 / Label seq-ID: 10 - 225

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

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Components

#1: Protein Carbonic anhydrase / Carbonate dehydratase


Mass: 26090.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neosartorya fumigata (strain ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100) (mold)
Strain: ATCC MYA-4609 / Af293 / CBS 101355 / FGSC A1100 / Gene: AFUA_8G06550 / Production host: Escherichia coli (E. coli) / References: UniProt: A4DA32, carbonic anhydrase
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2.66 Å3/Da / Density % sol: 53.73 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Tris-HCl pH 7.0-8.5 28-30% (w/v) polyethylene glycol 2000 (PEG2000) 0.1 M magnesium acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 27978 / % possible obs: 99.9 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.141 / Rpim(I) all: 0.049 / Rrim(I) all: 0.15 / Χ2: 0.643 / Net I/σ(I): 5.3 / Num. measured all: 246179
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.286.40.74327450.8960.3130.8070.4499.4
2.28-2.3770.6427530.9440.2550.690.43699.7
2.37-2.487.70.62827780.9630.2390.6730.43299.7
2.48-2.618.50.66627630.970.2390.7080.44199.9
2.61-2.779.20.5227790.9810.180.5510.47100
2.77-2.9990.36227850.9890.1280.3850.497100
2.99-3.29100.21727910.9950.0720.2290.556100
3.29-3.7610.50.13128120.9980.0420.1380.71100
3.76-4.7410.10.07928380.9990.0260.0830.974100
4.74-509.50.05829340.9990.020.0611.185100

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O1K

4o1k


Resolution: 2.2→41.08 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.919 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2144 1444 5.2 %RANDOM
Rwork0.1742 ---
obs0.1762 26517 98.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 143.28 Å2 / Biso mean: 47.749 Å2 / Biso min: 24.39 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20.67 Å20 Å2
2--1.34 Å2-0 Å2
3----4.34 Å2
Refinement stepCycle: final / Resolution: 2.2→41.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3494 0 8 143 3645
Biso mean--57.86 49.05 -
Num. residues----432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133576
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173304
X-RAY DIFFRACTIONr_angle_refined_deg1.4991.6374852
X-RAY DIFFRACTIONr_angle_other_deg1.3351.5737630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2455430
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95721.852216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10415608
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.8461530
X-RAY DIFFRACTIONr_chiral_restr0.0740.2454
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024022
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02780
Refine LS restraints NCS

Ens-ID: 1 / Number: 6657 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.204→2.261 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 95 -
Rwork0.261 1678 -
all-1773 -
obs--86.78 %

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