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

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Basic information

Entry
Database: PDB / ID: 4xix
TitleCarbonic anhydrase Cah3 from Chlamydomonas reinhardtii in complex with phosphate.
ComponentsCarbonic anhydrase, alpha type
KeywordsLYASE / 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 / Carbonic anhydrase
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 8, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 2.0Sep 13, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Derived calculations
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_validate_close_contact / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Jan 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

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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)212,41240
Polymers209,5618
Non-polymers2,85132
Water3,891216
1
A: Carbonic anhydrase, alpha type
G: Carbonic anhydrase, alpha type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,10310
Polymers52,3902
Non-polymers7138
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4540 Å2
ΔGint-142 kcal/mol
Surface area20340 Å2
MethodPISA
2
B: Carbonic anhydrase, alpha type
H: Carbonic anhydrase, alpha type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,20011
Polymers52,3902
Non-polymers8109
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-152 kcal/mol
Surface area20580 Å2
MethodPISA
3
C: Carbonic anhydrase, alpha type
E: Carbonic anhydrase, alpha type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,20011
Polymers52,3902
Non-polymers8109
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4690 Å2
ΔGint-142 kcal/mol
Surface area20650 Å2
MethodPISA
4
D: Carbonic anhydrase, alpha type
F: Carbonic anhydrase, alpha type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,9098
Polymers52,3902
Non-polymers5196
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-135 kcal/mol
Surface area20720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.957, 138.957, 202.807
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-2HP / DIHYDROGENPHOSPHATE ION / Dihydrogen phosphate


Mass: 96.987 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: H2O4P
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.1
Details: The protein solution (3.6 mg/mL) was mixed 1:1 with the reservoir that 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: 2.7→48.5 Å / Num. obs: 62714 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.3
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 8.8 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 2.4 / % possible all: 99.7

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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: 4xiw

4xiw


Resolution: 2.7→48.452 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 3171 5.07 %
Rwork0.1564 --
obs0.1601 62579 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→48.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14662 0 128 216 15006
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01715215
X-RAY DIFFRACTIONf_angle_d1.5620702
X-RAY DIFFRACTIONf_dihedral_angle_d15.0735590
X-RAY DIFFRACTIONf_chiral_restr0.0782224
X-RAY DIFFRACTIONf_plane_restr0.0082696
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.74040.40471280.31572555X-RAY DIFFRACTION99
2.7404-2.78320.37911440.28432542X-RAY DIFFRACTION99
2.7832-2.82880.381520.24232521X-RAY DIFFRACTION99
2.8288-2.87760.30821470.22532539X-RAY DIFFRACTION99
2.8776-2.92990.31591250.2112549X-RAY DIFFRACTION99
2.9299-2.98620.34971360.20222567X-RAY DIFFRACTION100
2.9862-3.04720.28071410.19812530X-RAY DIFFRACTION100
3.0472-3.11340.28091280.19242605X-RAY DIFFRACTION100
3.1134-3.18580.27791460.19452535X-RAY DIFFRACTION100
3.1858-3.26550.27581140.19822558X-RAY DIFFRACTION99
3.2655-3.35380.26071360.19892559X-RAY DIFFRACTION100
3.3538-3.45240.27831380.1712581X-RAY DIFFRACTION100
3.4524-3.56380.28981430.16722591X-RAY DIFFRACTION100
3.5638-3.69120.23771380.15052544X-RAY DIFFRACTION100
3.6912-3.83890.21811290.14082604X-RAY DIFFRACTION100
3.8389-4.01350.19581460.1342572X-RAY DIFFRACTION100
4.0135-4.2250.19421460.11812585X-RAY DIFFRACTION100
4.225-4.48950.15621420.10582605X-RAY DIFFRACTION100
4.4895-4.83590.16261280.10242619X-RAY DIFFRACTION100
4.8359-5.3220.15721360.10992617X-RAY DIFFRACTION100
5.322-6.09080.23771400.13282618X-RAY DIFFRACTION100
6.0908-7.66890.20121340.15152683X-RAY DIFFRACTION100
7.6689-48.45960.19591540.16492729X-RAY DIFFRACTION99

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