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- PDB-1y7w: Crystal structure of a halotolerant carbonic anhydrase from Dunal... -

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Basic information

Entry
Database: PDB / ID: 1y7w
TitleCrystal structure of a halotolerant carbonic anhydrase from Dunaliella salina
ComponentsHalotolerant alpha-type carbonic anhydrase (dCA II)
KeywordsLYASE / alpha-type carbonic anhydrase / haltolerant protein / algal carbonic anhydrase / salt tolerant protein / zinc enzyme / anion tolerance / Dunaliella salina carbonic anhydrase / dCA II / Israel Structural Proteomics Center / ISPC / Structural Genomics
Function / homologyCarbonic Anhydrase II / Alpha carbonic anhydrase / Roll / Alpha Beta / ACETIC ACID
Function and homology information
Biological speciesDunaliella salina (plant)
MethodX-RAY DIFFRACTION / MAD / Resolution: 1.86 Å
AuthorsPremkumar, L. / Greenblatt, H.M. / Bageshwar, U.K. / Savchenko, T. / Gokhman, I. / Sussman, J.L. / Zamir, A. / Israel Structural Proteomics Center (ISPC)
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Three-dimensional structure of a halotolerant algal carbonic anhydrase predicts halotolerance of a mammalian homolog.
Authors: Premkumar, L. / Greenblatt, H.M. / Bageshwar, U.K. / Savchenko, T. / Gokhman, I. / Sussman, J.L. / Zamir, A.
History
DepositionDec 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 23, 2023Group: 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_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE The sequence of the protein has not been deposited into any sequence database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Halotolerant alpha-type carbonic anhydrase (dCA II)
B: Halotolerant alpha-type carbonic anhydrase (dCA II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7709
Polymers63,4082
Non-polymers3627
Water9,494527
1
A: Halotolerant alpha-type carbonic anhydrase (dCA II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8534
Polymers31,7041
Non-polymers1483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Halotolerant alpha-type carbonic anhydrase (dCA II)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9185
Polymers31,7041
Non-polymers2144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-146 kcal/mol
Surface area22370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.022, 119.835, 58.442
Angle α, β, γ (deg.)90, 94.549, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Halotolerant alpha-type carbonic anhydrase (dCA II)


Mass: 31704.084 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dunaliella salina (plant) / Gene: dCA II / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / Strain (production host): Origami B pLysS / References: carbonic anhydrase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.65 Å3/Da / Density % sol: 52.7 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 2-propanol, PEG 4000, trisodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418, 1.28255, 1.28295, 0.9840
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 19, 2001
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.282551
31.282951
40.9841
ReflectionResolution: 1.86→35 Å / Num. all: 53986 / Num. obs: 53083 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.063 / Net I/σ(I): 28
Reflection shellResolution: 1.86→1.93 Å / % possible all: 90.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MAD
Starting model: PDB entry 2CAB

2cab


Resolution: 1.86→32.95 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2578 -RANDOM
Rwork0.167 ---
all0.194 53048 --
obs0.194 53048 98.1 %-
Displacement parametersBiso mean: 25.7 Å2
Baniso -1Baniso -2Baniso -3
1-6.77 Å20 Å24.15 Å2
2---2.64 Å20 Å2
3----4.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.86→32.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4212 0 13 527 4752
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.019
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d1.27
LS refinement shellResolution: 1.86→1.98 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.226 385 -
Rwork0.226 --
obs-7819 91.3 %

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