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- PDB-4xiw: Carbonic anhydrase Cah3 from Chlamydomonas reinhardtii in complex... -

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Basic information

Entry
Database: PDB / ID: 4xiw
TitleCarbonic anhydrase Cah3 from Chlamydomonas reinhardtii in complex with acetazolamide
ComponentsCarbonic anhydrase, alpha type
KeywordsLYASE / acetazolamide / photosystem II-associated
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
DIHYDROGENPHOSPHATE ION / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / Carbonic anhydrase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHainzl, T. / Grundstrom, C. / Benlloch, R. / Shevela, D. / Shutova, T. / Messinger, J. / Samuelsson, G. / Sauer-Eriksson, A.E.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council Sweden
CitationJournal: Plant Physiol. / Year: 2015
Title: Crystal Structure and Functional Characterization of Photosystem II-Associated Carbonic Anhydrase CAH3 in Chlamydomonas reinhardtii.
Authors: Benlloch, R. / Shevela, D. / Hainzl, T. / Grundstrom, C. / Shutova, T. / Messinger, J. / Samuelsson, G. / Sauer-Eriksson, A.E.
History
DepositionJan 7, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Jan 10, 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 / struct_conn
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
Revision 1.3Nov 13, 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: Carbonic anhydrase, alpha type
B: Carbonic anhydrase, alpha type
C: Carbonic anhydrase, alpha type
D: Carbonic anhydrase, alpha type
E: Carbonic anhydrase, alpha type
F: Carbonic anhydrase, alpha type
G: Carbonic anhydrase, alpha type
H: Carbonic anhydrase, alpha type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,41440
Polymers209,5618
Non-polymers3,85332
Water5,386299
1
A: Carbonic anhydrase, alpha type
G: Carbonic anhydrase, alpha type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,35410
Polymers52,3902
Non-polymers9638
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4850 Å2
ΔGint-123 kcal/mol
Surface area20330 Å2
MethodPISA
2
B: Carbonic anhydrase, alpha type
H: Carbonic anhydrase, alpha type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,45111
Polymers52,3902
Non-polymers1,0609
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-135 kcal/mol
Surface area20510 Å2
MethodPISA
3
C: Carbonic anhydrase, alpha type
E: Carbonic anhydrase, alpha type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,45111
Polymers52,3902
Non-polymers1,0609
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-122 kcal/mol
Surface area20790 Å2
MethodPISA
4
D: Carbonic anhydrase, alpha type
F: Carbonic anhydrase, alpha type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1608
Polymers52,3902
Non-polymers7696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-119 kcal/mol
Surface area20730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.356, 139.356, 203.209
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Carbonic anhydrase, alpha type / Intracellular carbonic anhydrase / alpha type


Mass: 26195.178 Da / Num. of mol.: 8 / Fragment: UNP residues 73-310
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CAH3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q39588
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / 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.: 8 / Source method: obtained synthetically / Formula: C4H6N4O3S2 / Comment: medication*YM
#4: Chemical
ChemComp-2HP / DIHYDROGENPHOSPHATE ION


Mass: 96.987 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: H2O4P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: The protein solution (3.6 mg/mL) was mixed with acetazolamide to a final concentration of 1 mM. The reservoir contained 2.5 M NH4H2PO4, 0.1 M Tris-HCl, pH 8.0. The final pH of the drop was 4.1.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.984 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.984 Å / Relative weight: 1
ReflectionResolution: 2.6→48.7 Å / Num. obs: 70627 / % possible obs: 99.9 % / Redundancy: 8.2 % / Rmerge(I) obs: 0.163 / Net I/σ(I): 9.1
Reflection shellResolution: 2.6→2.69 Å / Rmerge(I) obs: 0.957 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1koq

1koq


Resolution: 2.6→46.823 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 3551 5.04 %Random selection
Rwork0.1609 ---
obs0.1641 70441 99.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→46.823 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14657 0 192 299 15148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01815295
X-RAY DIFFRACTIONf_angle_d1.47620816
X-RAY DIFFRACTIONf_dihedral_angle_d15.7495644
X-RAY DIFFRACTIONf_chiral_restr0.0782224
X-RAY DIFFRACTIONf_plane_restr0.0082706
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.63560.33751360.25932646X-RAY DIFFRACTION99
2.6356-2.67330.32421350.25062667X-RAY DIFFRACTION100
2.6733-2.71320.32121340.24882647X-RAY DIFFRACTION99
2.7132-2.75560.33671410.24922580X-RAY DIFFRACTION99
2.7556-2.80080.35481300.23832669X-RAY DIFFRACTION99
2.8008-2.8490.33811230.22612669X-RAY DIFFRACTION99
2.849-2.90080.32261540.21572644X-RAY DIFFRACTION99
2.9008-2.95660.29331400.20982596X-RAY DIFFRACTION99
2.9566-3.0170.27331410.21192657X-RAY DIFFRACTION100
3.017-3.08260.30191320.21552701X-RAY DIFFRACTION100
3.0826-3.15420.28631530.2082646X-RAY DIFFRACTION100
3.1542-3.23310.33041420.20252622X-RAY DIFFRACTION99
3.2331-3.32050.28571600.19132655X-RAY DIFFRACTION100
3.3205-3.41820.22511390.17352656X-RAY DIFFRACTION100
3.4182-3.52850.22781500.1682642X-RAY DIFFRACTION100
3.5285-3.65450.25831320.16622688X-RAY DIFFRACTION100
3.6545-3.80080.21781230.15822716X-RAY DIFFRACTION100
3.8008-3.97370.23471570.15172671X-RAY DIFFRACTION100
3.9737-4.18310.20621540.13072652X-RAY DIFFRACTION100
4.1831-4.4450.19181580.11722696X-RAY DIFFRACTION100
4.445-4.78790.17431640.10232697X-RAY DIFFRACTION100
4.7879-5.26910.1611270.10672715X-RAY DIFFRACTION100
5.2691-6.03020.1681340.12392749X-RAY DIFFRACTION100
6.0302-7.59210.17461420.14972754X-RAY DIFFRACTION100
7.5921-46.70.18451500.16892855X-RAY DIFFRACTION99

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