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- PDB-4uov: The structure of a tetrameric alpha-carbonic anhydrase from Therm... -

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Basic information

Entry
Database: PDB / ID: 4uov
TitleThe structure of a tetrameric alpha-carbonic anhydrase from Thermovibrio ammonificans reveals a core formed around intermolecular disulfides, which contribute to its thermostability.
ComponentsCARBONATE DEHYDRATASE
KeywordsLYASE / CARBONIC ANHYDRASE / THERMOPHILIC / ACETAZOLAMIDE / CARBON DIOXIDE CAPTURE / THERMAL STABILITY.
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / zinc ion 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
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / Chem-PE3 / DI(HYDROXYETHYL)ETHER / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / TRIETHYLENE GLYCOL / L(+)-TARTARIC ACID / Carbonic anhydrase
Similarity search - Component
Biological speciesTHERMOVIBRIO AMMONIFICANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsJames, P. / Isupov, M. / Sayer, C. / Berg, S. / Lioliou, M. / Kotlar, H. / Littlechild, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: The Structure of a Tetrameric [Alpha]-Carbonic Anhydrase from Thermovibrio Ammonificans Reveals a Core Formed Around Intermolecular Disulfides that Contribute to its Thermostability
Authors: James, P. / Isupov, M.N. / Sayer, C. / Saneei, V. / Berg, S. / Lioliou, M. / Kotlar, H. / Littlechild, J.
History
DepositionJun 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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_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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBONATE DEHYDRATASE
B: CARBONATE DEHYDRATASE
C: CARBONATE DEHYDRATASE
D: CARBONATE DEHYDRATASE
E: CARBONATE DEHYDRATASE
F: CARBONATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,73464
Polymers166,3556
Non-polymers8,37858
Water34,5531918
1
E: CARBONATE DEHYDRATASE
F: CARBONATE DEHYDRATASE
hetero molecules

E: CARBONATE DEHYDRATASE
F: CARBONATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,87144
Polymers110,9044
Non-polymers5,96740
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area11750 Å2
ΔGint-312.3 kcal/mol
Surface area38960 Å2
MethodPISA
2
A: CARBONATE DEHYDRATASE
B: CARBONATE DEHYDRATASE
C: CARBONATE DEHYDRATASE
D: CARBONATE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,29842
Polymers110,9044
Non-polymers5,39538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13340 Å2
ΔGint-295 kcal/mol
Surface area39710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.750, 283.020, 52.170
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99307, 0.11728, 0.00769), (-0.11738, -0.99298, -0.01474), (0.00591, -0.01554, 0.99986)-88.86851, 131.69994, 1.93302
2given(-0.5614, -0.82753, -0.00476), (-0.82747, 0.56142, -0.00987), (0.01084, -0.0016, -0.99994)-6.36799, -3.4332, 0.12025
3given(0.46508, 0.88526, 0.00431), (0.8851, -0.46508, 0.01742), (0.01743, -0.00428, -0.99984)-82.43396, 136.08701, 1.05598
4given(0.53081, -0.84749, -0.00018), (-0.84749, -0.53081, -0.00098), (0.00074, 0.00067, -1)79.47558, 143.34244, -0.41981
5given(0.37383, -0.92744, -0.01044), (0.92745, 0.37368, 0.01385), (-0.00895, -0.01486, 0.99985)78.56078, 153.68517, 0.95133

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
CARBONATE DEHYDRATASE / ALPHA CARBONIC ANHYDRASE


Mass: 27725.900 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Details: DSMZ / Source: (natural) THERMOVIBRIO AMMONIFICANS (bacteria) / References: UniProt: E8T502, carbonic anhydrase

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Non-polymers , 11 types, 1976 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE


Mass: 222.245 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6N4O3S2 / Comment: medication*YM
#4: Chemical ChemComp-PE3 / 3,6,9,12,15,18,21,24,27,30,33,36,39-TRIDECAOXAHENTETRACONTANE-1,41-DIOL / POLYETHYLENE GLYCOL


Mass: 634.751 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H58O15
#5: Chemical
ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: Cl
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H6O6
#10: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#11: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1918 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.66 Å3/Da / Density % sol: 66 % / Description: NONE
Crystal growpH: 5.5
Details: 9% ETHYLENE GLYCOL, 9 % PEG8000, 10 MM CARBOXYLIC ACIDS ADDITIVE MIXTURE, 100MM MES PH 6.5.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Aug 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.85→42.01 Å / Num. obs: 206954 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.7
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.95 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C3T

4c3t


Resolution: 1.85→42.01 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.657 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. LOCAL NCS RESTRICTIONS WERE APPLIED THROUGHOUT REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.20404 10399 5 %RANDOM
Rwork0.17181 ---
obs0.17341 196389 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.828 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.8 Å20 Å2
3---1.2 Å2
Refinement stepCycle: LAST / Resolution: 1.85→42.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10878 0 435 1918 13231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01912801
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.98317500
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74251693
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.48523.317615
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.177152292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4711595
X-RAY DIFFRACTIONr_chiral_restr0.1140.21781
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219895
X-RAY DIFFRACTIONr_gen_planes_other
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_it3.0976.4845756
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.87710.8737275
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8437.3917043
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 791 -
Rwork0.277 14251 -
obs--99.56 %

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