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- PDB-3q31: Structure of fungal alpha Carbonic Anhydrase from Aspergillus oryzae -

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Basic information

Entry
Database: PDB / ID: 3q31
TitleStructure of fungal alpha Carbonic Anhydrase from Aspergillus oryzae
ComponentsCarbonic anhydrase
KeywordsLYASE / Alpha Carbonic Anhydrase / Fungal Carbonic Anhydrase / glysosylation / Secreted / Dimeric
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / zinc ion binding / identical protein binding
Similarity search - Function
Carbonic anhydrase, prokaryotic-like / Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. ...Carbonic anhydrase, prokaryotic-like / Carbonic Anhydrase II / Alpha carbonic anhydrase / Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase / Roll / Alpha Beta
Similarity search - Domain/homology
D-MALATE / Carbonic anhydrase
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å
AuthorsCuesta-Seijo, J.A. / Borchert, M.S. / Navarro-Poulsen, J.C. / Schnorr, K.M. / Leggio, L.L.
CitationJournal: To be Published
Title: Structure of fungal alpha Carbonic Anhydrase from Aspergillus oryzae
Authors: Cuesta-Seijo, J.A. / Borchert, M.S. / Navarro-Poulsen, J.C. / Schnorr, K.M. / Leggio, L.L.
History
DepositionDec 21, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 23, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)53,7748
Polymers52,9332
Non-polymers8416
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-18 kcal/mol
Surface area18740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.240, 80.240, 247.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (not (resid 242:244))
211chain B

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Components

#1: Protein Carbonic anhydrase


Mass: 26466.402 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 27-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Gene: AO090010000582 / Production host: Aspergillus oryzae (mold) / References: UniProt: Q2TWF5, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 3.76 Å3/Da / Density % sol: 67.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2.2M ammonium sulphate, 0.1M buffersystem II pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03796 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 11, 2009 / Details: Mirrors
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03796 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. all: 22846 / Num. obs: 22846 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.14 % / Biso Wilson estimate: 36.56 Å2 / Rsym value: 0.1078 / Net I/σ(I): 11.43
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 6.14 % / Mean I/σ(I) obs: 2.7 / Num. unique all: 2204 / Rsym value: 0.404 / % possible all: 98.4

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KOP

1kop


Resolution: 2.703→19.801 Å / SU ML: 0.3 / Isotropic thermal model: Isotropic, TLS / Cross valid method: THROUGHOUT / σ(F): 0.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2532 999 5.13 %Random
Rwork0.209 ---
all0.2112 19481 --
obs0.2112 19481 84.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 24.655 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso mean: 43.76 Å2
Baniso -1Baniso -2Baniso -3
1-11.7668 Å20 Å2-0 Å2
2--11.7668 Å20 Å2
3----23.5337 Å2
Refinement stepCycle: LAST / Resolution: 2.703→19.801 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 48 91 3785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013864
X-RAY DIFFRACTIONf_angle_d1.3845258
X-RAY DIFFRACTIONf_dihedral_angle_d21.7341344
X-RAY DIFFRACTIONf_chiral_restr0.091584
X-RAY DIFFRACTIONf_plane_restr0.005690
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1832X-RAY DIFFRACTIONPOSITIONAL
12B1832X-RAY DIFFRACTIONPOSITIONAL0.052
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7029-2.8450.39491330.345202067
2.845-3.02260.33161170.3156224474
3.0226-3.25510.35391400.2771245080
3.2551-3.58090.25251530.2247268188
3.5809-4.09510.22981630.1766286792
4.0951-5.14440.17811440.1463303796
5.1444-19.8020.2061490.1871318395

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