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- PDB-6jqc: The structural basis of the beta-carbonic anhydrase CafC (wild ty... -

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Basic information

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


carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Beta-carbonic Anhydrase; Chain A / Carbonic anhydrase / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNeosartorya fumigata (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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_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)36,4304
Polymers36,2992
Non-polymers1312
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7310 Å2
ΔGint-115 kcal/mol
Surface area14360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.575, 80.066, 48.791
Angle α, β, γ (deg.)90.00, 115.84, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 0 / Auth seq-ID: 1 - 164 / Label seq-ID: 1 - 164

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

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Components

#1: Protein Carbonic anhydrase / / Carbonate dehydratase


Mass: 18149.645 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_4G09420 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4WPJ0, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.06 Å3/Da / Density % sol: 40.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 1-11% PEG2000 and 100 mM sodium acetate pH 4.5-5.5

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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: Sep 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 24771 / % possible obs: 91.5 % / Redundancy: 2.6 % / Rpim(I) all: 0.069 / Net I/σ(I): 17.6
Reflection shellResolution: 1.8→1.86 Å / Num. unique obs: 2463 / Rpim(I) all: 0.311

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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: 1G5C
Resolution: 1.8→40.07 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.034 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.161 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24909 1190 4.8 %RANDOM
Rwork0.19785 ---
obs0.2003 23562 91.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 23.668 Å2
Baniso -1Baniso -2Baniso -3
1-1 Å2-0 Å2-0.12 Å2
2---0.62 Å20 Å2
3----0.18 Å2
Refinement stepCycle: 1 / Resolution: 1.8→40.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2544 0 2 205 2751
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132584
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172490
X-RAY DIFFRACTIONr_angle_refined_deg1.6621.6423486
X-RAY DIFFRACTIONr_angle_other_deg1.3471.5825712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.40120.128156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86115454
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9211532
X-RAY DIFFRACTIONr_chiral_restr0.0720.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022940
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02580
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_it1.8442.2731310
X-RAY DIFFRACTIONr_mcbond_other1.8412.271309
X-RAY DIFFRACTIONr_mcangle_it2.7183.3971634
X-RAY DIFFRACTIONr_mcangle_other2.7183.41635
X-RAY DIFFRACTIONr_scbond_it2.6632.6621274
X-RAY DIFFRACTIONr_scbond_other2.6612.6561271
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2273.8571852
X-RAY DIFFRACTIONr_long_range_B_refined5.84727.6532817
X-RAY DIFFRACTIONr_long_range_B_other5.75127.3572784
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4694 / 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: 1.804→1.851 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 83 -
Rwork0.252 1678 -
obs--88.94 %

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