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- PDB-3bob: Carbonic anhydrase from marine diatom Thalassiosira weissflogii- ... -

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Basic information

Entry
Database: PDB / ID: 3bob
TitleCarbonic anhydrase from marine diatom Thalassiosira weissflogii- cadmium bound domain 2
ComponentsCadmium-specific carbonic anhydrase
KeywordsLYASE / carbonic anhydrase / marine diatom / cadmium-bound
Function / homologyCadmium carbonic anhydrase repeat / Cadmium carbonic anhydrase repeat / metal ion binding / : / Cadmium-specific carbonic anhydrase
Function and homology information
Biological speciesThalassiosira weissflogii (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsXu, Y. / Feng, L. / Jeffrey, P.D. / Shi, Y. / Morel, F.M.M.
CitationJournal: Nature / Year: 2008
Title: Structure and metal exchange in the cadmium carbonic anhydrase of marine diatoms.
Authors: Xu, Y. / Feng, L. / Jeffrey, P.D. / Shi, Y. / Morel, F.M.
History
DepositionDec 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cadmium-specific carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5452
Polymers22,4321
Non-polymers1121
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.283, 78.202, 37.054
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1203-

HOH

21A-1217-

HOH

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Components

#1: Protein Cadmium-specific carbonic anhydrase


Mass: 22432.449 Da / Num. of mol.: 1 / Fragment: Domain 2, CDCA1-R2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thalassiosira weissflogii (Diatom) / Gene: cdca1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q50EL4, carbonic anhydrase
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRELATIVE TO THE ORIGINAL COORDINATES THE CADMIUM AND WATER MOLECULE NUMBERING HAS BEEN OFFSET BY ...RELATIVE TO THE ORIGINAL COORDINATES THE CADMIUM AND WATER MOLECULE NUMBERING HAS BEEN OFFSET BY 1000, AND THE CHAIN LABEL HAS BEEN SET TO THAT OF THE POLYPEPTIDE CHAIN.

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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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium citrate, 20% (w/v) PEG3350, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 13, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. all: 35966 / Num. obs: 35966 / % possible obs: 95.4 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.073
Reflection shellResolution: 1.4→1.45 Å / Rsym value: 0.443 / % possible all: 92.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→24.83 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1029413.41 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1615 5 %RANDOM
Rwork0.167 ---
obs0.167 32511 95.7 %-
all-32511 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.3147 Å2 / ksol: 0.364366 e/Å3
Displacement parametersBiso mean: 18.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.02 Å20 Å20 Å2
2---1.08 Å20 Å2
3----2.94 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.16 Å0.14 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.45→24.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1568 0 1 250 1819
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.042.5
X-RAY DIFFRACTIONc_mcangle_it2.513
X-RAY DIFFRACTIONc_scbond_it3.693
X-RAY DIFFRACTIONc_scangle_it4.883.5
LS refinement shellResolution: 1.45→1.54 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.232 244 4.7 %
Rwork0.209 4991 -
obs--93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4cadmium.param

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