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- PDB-6gwu: Carbonic anhydrase CaNce103p from Candida albicans -

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Basic information

Entry
Database: PDB / ID: 6gwu
TitleCarbonic anhydrase CaNce103p from Candida albicans
ComponentsCarbonic anhydrase
KeywordsLYASE / Carbonic anhydrase / Candida albicans / CaNce103p / substrate tunnel
Function / homology
Function and homology information


regulation of phenotypic switching / phenotypic switching / cellular response to carbon dioxide / carbon utilization / carbonic anhydrase / carbonate dehydratase activity / mitochondrial intermembrane space / cellular response to oxidative stress / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Prokaryotic-type carbonic anhydrases signature 2. / Carbonic anhydrase, prokaryotic-like, conserved site / 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
BETA-MERCAPTOETHANOL / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Carbonic anhydrase
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBrynda, J. / Dostal, J. / Heidingsfeld, O. / Machacek, S. / Blaha, J. / Pichova, I.
Funding support Czech Republic, 2items
OrganizationGrant numberCountry
Czech Science FoundationGA17-08343S Czech Republic
Ministry of Education (Czech Republic)LO1302 Czech Republic
CitationJournal: BMC Struct. Biol. / Year: 2018
Title: Crystal structure of carbonic anhydrase CaNce103p from the pathogenic yeast Candida albicans.
Authors: Dostal, J. / Brynda, J. / Blaha, J. / Machacek, S. / Heidingsfeld, O. / Pichova, I.
History
DepositionJun 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 7, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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
C: Carbonic anhydrase
D: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,19815
Polymers92,2614
Non-polymers93711
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18530 Å2
ΔGint-287 kcal/mol
Surface area31810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.363, 90.280, 167.105
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
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
11ASNASNPROPROAA26 - 2291 - 204
21ASNASNPROPROBB26 - 2291 - 204
12ASNASNILEILEAA26 - 2281 - 203
22ASNASNILEILECC26 - 2281 - 203
13PHEPHESERSERAA27 - 2242 - 199
23PHEPHESERSERDD27 - 2242 - 199
14ASNASNILEILEBB26 - 2281 - 203
24ASNASNILEILECC26 - 2281 - 203
15PHEPHESERSERBB27 - 2242 - 199
25PHEPHESERSERDD27 - 2242 - 199
16PHEPHESERSERCC27 - 2242 - 199
26PHEPHESERSERDD27 - 2242 - 199

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Carbonic anhydrase / Carbonate dehydratase / Non-classical export protein 103


Mass: 23065.328 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: NCE103, CAALFM_C301300CA, CaO19.1721, CaO19.9289 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5AJ71, carbonic anhydrase

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Non-polymers , 5 types, 46 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 2.84 Å3/Da / Density % sol: 56.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M ammonium acetate or 0.2 M magnesium chloride, 0.1 M Bis-Tris, pH 5.5, 25% (w/v) PEG 3350 or 45% (w/v) MPD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jan 8, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.2→45.94 Å / Num. obs: 53038 / % possible obs: 98.1 % / Redundancy: 4.478 % / Biso Wilson estimate: 49.031 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.165 / Rrim(I) all: 0.187 / Χ2: 1.012 / Net I/σ(I): 8.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.334.5712.3280.8384390.6082.62598.2
2.33-2.494.4071.5461.2279150.6991.75397.5
2.49-2.694.6070.961.9274340.7471.08298.3
2.69-2.954.5340.4733.6668660.9340.53698.6
2.95-3.294.4190.2516.2462490.9710.28598.1
3.29-3.84.5320.12211.6455670.9930.13998.7
3.8-4.654.4330.05621.7646890.9980.06497.7
4.65-6.544.3450.04924.7736880.9980.05697.3
6.54-45.944.1070.02738.3621900.9990.03197.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O1J

4o1j


Resolution: 2.2→45.94 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.888 / SU B: 27.386 / SU ML: 0.285 / SU R Cruickshank DPI: 0.2557 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.256 / ESU R Free: 0.214
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.279 809 1.5 %RANDOM
Rwork0.2406 ---
obs0.2412 52491 98.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 204.9 Å2 / Biso mean: 80.881 Å2 / Biso min: 46.14 Å2
Baniso -1Baniso -2Baniso -3
1--5.44 Å20 Å2-0 Å2
2--3.15 Å20 Å2
3---2.29 Å2
Refinement stepCycle: final / Resolution: 2.2→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6198 0 36 35 6269
Biso mean--85.5 62.27 -
Num. residues----819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196344
X-RAY DIFFRACTIONr_bond_other_d0.0080.026125
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9458606
X-RAY DIFFRACTIONr_angle_other_deg2.494314021
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8635814
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.44825.192260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.842151042
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5021520
X-RAY DIFFRACTIONr_chiral_restr0.0920.21004
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027243
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021445
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A209480.2
12B209480.2
21A197000.21
22C197000.21
31A200920.21
32D200920.21
41B195480.22
42C195480.22
51B200480.21
52D200480.21
61C192200.21
62D192200.21
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.434 59 -
Rwork0.431 3835 -
all-3894 -
obs--98.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0215-0.0072-0.19020.00410.06911.94-0.00230.05480.00120.0283-0.0111-0.00690.1346-0.19630.01340.7069-0.0065-0.01260.4974-0.00180.0645-23.8403-1.388-34.6532
20.03110.00340.22010.00390.00251.71950.00380.05250.0050.02540.02520.0126-0.07860.2051-0.0290.7210.01330.02640.5131-0.00170.0581-10.08445.1877-34.403
30.10580.035-0.6090.0136-0.223.690.1212-0.10950.01610.0179-0.01010.009-0.38580.545-0.11110.714-0.07590.0250.5923-0.03520.0264-13.42564.8659-72.1157
40.0033-0.0012-0.02190.02470.29253.50050.0459-0.00840.00220.0126-0.0326-0.00140.0797-0.2992-0.01330.6591-0.01560.03080.46420.00010.0521-25.7001-3.0499-72.0391
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 301
2X-RAY DIFFRACTION2B26 - 301
3X-RAY DIFFRACTION3C26 - 301
4X-RAY DIFFRACTION4D27 - 301

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