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- PDB-3b1b: The unique structure of wild type carbonic anhydrase alpha-CA1 fr... -

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Basic information

Entry
Database: PDB / ID: 3b1b
TitleThe unique structure of wild type carbonic anhydrase alpha-CA1 from Chlamydomonas reinhardtii
ComponentsCarbonic anhydrase 1
KeywordsLYASE / N-glycosylation / zinc-finger / carbonic anhydrase
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / periplasmic space / 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
Carbonic anhydrase 1
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.88 Å
AuthorsShimizu, S. / Takenaka, A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: The unique structure of carbonic anhydrase alpha CA1 from Chlamydomonas reinhardtii
Authors: Suzuki, K. / Yang, S.Y. / Shimizu, S. / Morishita, E.C. / Jiang, J. / Zhang, F. / Hoque, M.M. / Sato, Y. / Tsunoda, M. / Sekiguchi, T. / Takenaka, A.
History
DepositionJun 29, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Jun 24, 2020Group: Advisory / Data collection / Derived calculations / Category: chem_comp / database_PDB_caveat / struct_conn
Item: _chem_comp.type / _database_PDB_caveat.text / _struct_conn.pdbx_leaving_atom_flag
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 / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_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_seq_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_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_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 1
B: Carbonic anhydrase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,88712
Polymers83,3622
Non-polymers1,52510
Water15,997888
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4970 Å2
ΔGint-121 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.3, 134.3, 120.1
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Carbonic anhydrase 1 / Carbonate dehydratase 1 / CA1


Mass: 41680.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P20507, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 888 / 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: 3.75 Å3/Da / Density % sol: 67.21 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.0-2.0M Ammonium sulfate, 100mM Tris-HCl (pH8.5), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1.00, 1.28254, 1.28297
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 27, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.282541
31.282971
ReflectionResolution: 1.88→50 Å / Num. obs: 99548 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 60
Reflection shellResolution: 1.88→1.95 Å / Redundancy: 10 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 8.7 / Num. unique all: 9936 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.88→41.3 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.374 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: TREATMENT OF N-ACETYLGLUCANS THE THREE SUGAR MOIETIES BOUND TO THE ASPARAGINE RESIDUES OF A SUBUNIT ARE ASSUMED TO BE N-ACETYLGLUCANS THOUGH THE ELECTRON DENSITY SUGGESTS LARGER GLUCANS. IN ...Details: TREATMENT OF N-ACETYLGLUCANS THE THREE SUGAR MOIETIES BOUND TO THE ASPARAGINE RESIDUES OF A SUBUNIT ARE ASSUMED TO BE N-ACETYLGLUCANS THOUGH THE ELECTRON DENSITY SUGGESTS LARGER GLUCANS. IN THE REFINEMENT, HOWEVER, THESE MOIETIES WERE REFINED WITHOUT GEOMETRICAL RESTRAINS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21757 4965 5 %RANDOM
Rwork0.18736 ---
obs0.18886 94307 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.288 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20.56 Å20 Å2
2--1.12 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 1.88→41.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4859 0 87 888 5834
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0215128
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5461.9486990
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5355630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.36424.444243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.81215794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3021526
X-RAY DIFFRACTIONr_chiral_restr0.1140.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023948
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.22295
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3070.23433
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2731
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1640.22
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.231
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9881.53177
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.6625011
X-RAY DIFFRACTIONr_scbond_it2.39632222
X-RAY DIFFRACTIONr_scangle_it3.6674.51973
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.881→1.93 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 394 -
Rwork0.243 6923 -
obs-6927 99.97 %

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