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- PDB-7cxy: Structural insights into novel mechanisms of inhibition of the ma... -

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Basic information

Entry
Database: PDB / ID: 7cxy
TitleStructural insights into novel mechanisms of inhibition of the major b-carbonic anhydrase CafB from the pathogenic fungus Aspergillus fumigatus (zinc-bound 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
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)52,1284
Polymers51,9972
Non-polymers1312
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6220 Å2
ΔGint-43 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.862, 119.862, 67.587
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 16 - 221 / Label seq-ID: 16 - 221

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

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Components

#1: Protein Carbonic anhydrase / Carbonate dehydratase


Mass: 25998.557 Da / Num. of mol.: 2 / Mutation: Y159A
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-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.: 136 / 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: 2.69 Å3/Da / Density % sol: 54.21 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate pH 4-5 1.7-2.0 M sodium chloride 10 mM Tris(2-carboxyethyl)phosphine hydrochloride (TCEP)

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 28654 / % possible obs: 100 % / Redundancy: 12.1 % / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.077 / Rrim(I) all: 0.27 / Χ2: 1.169 / Net I/σ(I): 3.8 / Num. measured all: 347292
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.288.41.46928230.7530.5191.5610.585100
2.28-2.379.71.25828450.8230.4121.3260.51999.9
2.37-2.4811.61.14128310.9150.3461.1930.649100
2.48-2.6112.51.03828470.9390.3031.0820.564100
2.61-2.7712.80.74828310.9640.2160.7790.589100
2.77-2.9913.20.46428530.9720.1320.4830.61599.9
2.99-3.2913.70.28828500.990.080.2990.766100
3.29-3.7612.80.16528870.9930.0470.1721.103100
3.76-4.7413.80.11628870.9940.0320.122.02100
4.74-5012.60.130000.9920.0290.1043.704100

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Processing

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

4o1k


Resolution: 2.2→44.88 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 5.924 / SU ML: 0.144 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 1409 4.9 %RANDOM
Rwork0.1837 ---
obs0.1858 27227 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.26 Å2 / Biso mean: 43.963 Å2 / Biso min: 9.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.4 Å20 Å2
2--0.8 Å2-0 Å2
3----2.59 Å2
Refinement stepCycle: final / Resolution: 2.2→44.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3396 0 2 136 3534
Biso mean--30.91 42.27 -
Num. residues----421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133473
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173210
X-RAY DIFFRACTIONr_angle_refined_deg1.6791.6414710
X-RAY DIFFRACTIONr_angle_other_deg1.3121.5747413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.395419
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.00821.762210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.10315593
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3551530
X-RAY DIFFRACTIONr_chiral_restr0.0720.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023914
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02760
Refine LS restraints NCS

Ens-ID: 1 / Number: 6356 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.202→2.259 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 112 -
Rwork0.269 1992 -
all-2104 -
obs--99.62 %

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