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- PDB-7coj: Crystal structure of the b-carbonic anhydrase CafA of the fungal ... -

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Basic information

Entry
Database: PDB / ID: 7coj
TitleCrystal structure of the b-carbonic anhydrase CafA of the fungal pathogen Aspergillus fumigatus
ComponentsCarbonic anhydrase
KeywordsLYASE / b-class carbonic anhydrase / CafA / zinc metalloenzyme / Aspergillus fumigatus
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 2. / Carbonic anhydrase, prokaryotic-like, conserved site / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase
Similarity search - Domain/homology
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / Carbonic anhydrase
Similarity search - Component
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJin, M.S. / Kim, S. / Yeon, J. / Sung, J.
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: Mol.Cells / Year: 2020
Title: Crystal Structure of beta-Carbonic Anhydrase CafA from the Fungal Pathogen Aspergillus fumigatus .
Authors: Kim, S. / Yeon, J. / Sung, J. / Jin, M.S.
History
DepositionAug 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)124,62112
Polymers123,4704
Non-polymers1,1518
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19450 Å2
ΔGint-272 kcal/mol
Surface area30880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.921, 87.953, 144.717
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERTHRTHRAA78 - 28578 - 285
21SERSERTHRTHRBB78 - 28578 - 285
12SERSERASPASPAA76 - 28676 - 286
22SERSERASPASPCC76 - 28676 - 286
13ASPASPTHRTHRAA79 - 28579 - 285
23ASPASPTHRTHRDD79 - 28579 - 285
14SERSERTHRTHRBB78 - 28578 - 285
24SERSERTHRTHRCC78 - 28578 - 285
15ASPASPTHRTHRBB79 - 28579 - 285
25ASPASPTHRTHRDD79 - 28579 - 285
16ASPASPTHRTHRCC79 - 28579 - 285
26ASPASPTHRTHRDD79 - 28579 - 285

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Carbonic anhydrase / Carbonate dehydratase


Mass: 30867.516 Da / Num. of mol.: 4
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_4G11250 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4WQ18, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE


Mass: 222.245 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C4H6N4O3S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 1.72 Å3/Da / Density % sol: 28.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.1 M MES (or Tris-HCl) pH 6.0-7.5 24-30% (w/v) PEG2000MME 0.2-0.4 M sodium acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 58640 / % possible obs: 99.9 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.032 / Rrim(I) all: 0.085 / Χ2: 2.494 / Net I/σ(I): 12.8 / Num. measured all: 417852
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.077.20.30657640.9750.1230.331.922100
2.07-2.157.20.23957890.9840.0960.2582.023100
2.15-2.257.20.19158210.9860.0760.2062.202100
2.25-2.377.30.16157820.9910.0640.1732.218100
2.37-2.527.30.1358220.9940.0520.142.355100
2.52-2.717.20.10358370.9960.0410.1112.524100
2.71-2.997.20.08458740.9960.0340.092.66100
2.99-3.427.10.06858790.9970.0280.0742.812100
3.42-4.3170.05659550.9980.0230.0613.096100
4.31-506.50.05461170.9970.0230.0593.16898.6

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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→33.48 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.943 / SU B: 3.294 / SU ML: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2046 2919 5 %RANDOM
Rwork0.161 ---
obs0.1631 55669 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 121.15 Å2 / Biso mean: 29.166 Å2 / Biso min: 14.93 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å20 Å20 Å2
2---0.49 Å20 Å2
3----2.04 Å2
Refinement stepCycle: final / Resolution: 2→33.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6427 0 56 522 7005
Biso mean--27.61 34.28 -
Num. residues----840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136623
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176356
X-RAY DIFFRACTIONr_angle_refined_deg1.6881.638982
X-RAY DIFFRACTIONr_angle_other_deg1.4331.57514730
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7615842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.25222.152316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.264151156
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1861544
X-RAY DIFFRACTIONr_chiral_restr0.0870.2851
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027393
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021291
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumber
11A6364
12B6364
21A6430
22C6430
31A6337
32D6337
41B6389
42C6389
51B6375
52D6375
61C6382
62D6382
LS refinement shellResolution: 2→2.048 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.223 200 -
Rwork0.189 3930 -
obs--95.89 %

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