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- PDB-6lai: The structural basis of the beta-carbonic anhydrase CafD (E54A mu... -

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Basic information

Entry
Database: PDB / ID: 6lai
TitleThe structural basis of the beta-carbonic anhydrase CafD (E54A mutant) 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: 1.6 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: To be published
Title: The structural analysis of non-catalytic zinc binding site in the minor beta-carbonic anhydrase CafD
Authors: Jin, M.S. / Kim, S. / Kim, N.J. / Hong, S. / Kim, S. / Sung, J.
History
DepositionNov 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,4754
Polymers40,3442
Non-polymers1312
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-18 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.048, 57.629, 73.306
Angle α, β, γ (deg.)90.000, 111.840, 90.000
Int Tables number5
Space group name H-MC121
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: GLU / End label comp-ID: GLU / Refine code: _ / Auth seq-ID: 9 - 180 / Label seq-ID: 9 - 180

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

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Components

#1: Protein Carbonic anhydrase / Carbonate dehydratase


Mass: 20171.896 Da / Num. of mol.: 2 / Mutation: E54A
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.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.04 Å3/Da / Density % sol: 39.77 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 28 % PEG3350, 200 mM MgCl2, 100 mM Tris-HCl pH 6.0-9.5

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Data collection

DiffractionMean temperature: 77 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 29, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 40349 / % possible obs: 98.4 % / Redundancy: 3.4 % / Rsym value: 0.08 / Net I/σ(I): 22.5
Reflection shellResolution: 1.6→1.66 Å / Num. unique obs: 4253 / Rsym value: 0.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JQE

6jqe


Resolution: 1.6→46.4 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 1.673 / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.218 2065 4.9 %RANDOM
Rwork0.183 ---
obs0.1846 40349 98.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 94.23 Å2 / Biso mean: 24.525 Å2 / Biso min: 11.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 1.6→46.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2688 0 2 145 2835
Biso mean--13.65 29.24 -
Num. residues----344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132743
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172520
X-RAY DIFFRACTIONr_angle_refined_deg1.7571.6333712
X-RAY DIFFRACTIONr_angle_other_deg1.5131.5775842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5335342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.24122.133150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.90215482
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6971522
X-RAY DIFFRACTIONr_chiral_restr0.0870.2348
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02564
Refine LS restraints NCS

Ens-ID: 1 / Number: 5148 / 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: 1.6→1.64 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.256 162 -
Rwork0.216 2965 -
obs--98.21 %

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