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- PDB-6jqe: The structural basis of the beta-carbonic anhydrases CafD (wild t... -

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Basic information

Entry
Database: PDB / ID: 6jqe
TitleThe structural basis of the beta-carbonic anhydrases CafD (wild type) of the filamentous fungus Aspergillus fumigatus
ComponentsCarbonic anhydrase
KeywordsLYASE / beta-class carbonic anhydrase / Aspergillus fumigatus / CafD
Function / homology
Function and homology information


cellular response to carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / cellular response to oxidative stress / zinc ion binding / cytoplasm
Similarity search - Function
Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase
Similarity search - Domain/homology
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJin, M.S. / Kim, S. / Kim, N.J. / Hong, S. / Kim, S. / Sung, J.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (Korea)NRF-2017R1A2B4003278 Korea, Republic Of
National Research Foundation (Korea)NRF-2017M3A9F6029753 Korea, Republic Of
CitationJournal: J.Struct.Biol. / Year: 2019
Title: The structural basis of the low catalytic activities of the two minor beta-carbonic anhydrases of the filamentous fungus Aspergillus fumigatus.
Authors: Kim, S. / Kim, N.J. / Hong, S. / Kim, S. / Sung, J. / Jin, M.S.
History
DepositionMar 30, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: 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_conn.ptnr2_label_seq_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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)38,4555
Polymers38,2592
Non-polymers1963
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-60 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.240, 57.298, 73.147
Angle α, β, γ (deg.)90.00, 112.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-344-

HOH

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

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: TYR / Beg label comp-ID: TYR / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: _ / Auth seq-ID: 9 - 179 / Label seq-ID: 1 - 171

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

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Components

#1: Protein Carbonic anhydrase / Carbonate dehydratase


Mass: 19129.621 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_8G06554 / Production host: Escherichia coli (E. coli) / References: UniProt: A4DA31, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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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: 2.14 Å3/Da / Density % sol: 42.45 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 24-28% PEG3350, 200 mM MgCl2 and 100 mM HEPES pH 7.0-7.5

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 24, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 22753 / % possible obs: 94 % / Redundancy: 2.6 % / Rpim(I) all: 0.077 / Net I/σ(I): 18.7
Reflection shellResolution: 1.9→1.97 Å / Num. unique obs: 2375 / Rpim(I) all: 0.455

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JOR

6jor
PDB Unreleased entry


Resolution: 1.9→46.23 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.622 / SU ML: 0.131 / Cross valid method: THROUGHOUT / ESU R: 0.198 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25249 1157 4.8 %RANDOM
Rwork0.20546 ---
obs0.20769 22753 93.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 38.562 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å20.06 Å2
2--0.91 Å2-0 Å2
3---0.78 Å2
Refinement stepCycle: 1 / Resolution: 1.9→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2678 0 3 93 2774
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132735
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172506
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.6333694
X-RAY DIFFRACTIONr_angle_other_deg1.3411.5765816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6925340
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.83122.133150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28215482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4711522
X-RAY DIFFRACTIONr_chiral_restr0.0770.2346
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023064
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4343.7711366
X-RAY DIFFRACTIONr_mcbond_other3.4133.771365
X-RAY DIFFRACTIONr_mcangle_it4.9485.641704
X-RAY DIFFRACTIONr_mcangle_other4.9475.6411705
X-RAY DIFFRACTIONr_scbond_it4.7864.3961369
X-RAY DIFFRACTIONr_scbond_other4.7864.3961369
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4556.3571991
X-RAY DIFFRACTIONr_long_range_B_refined9.69144.3182997
X-RAY DIFFRACTIONr_long_range_B_other9.69544.2592981
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5100 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.09 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 74 -
Rwork0.277 1563 -
obs--86.84 %

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