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

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Basic information

Entry
Database: PDB / ID: 3boj
TitleCarbonic anhydrase from marine diatom Thalassiosira weissflogii- cadmium bound domain 1 without bound metal (CDCA1-R1)
ComponentsCadmium-specific carbonic anhydrase
KeywordsLYASE / carbonic anhydrase / marine diatom / apo form
Function / homologyCadmium carbonic anhydrase repeat / Cadmium carbonic anhydrase repeat / metal ion binding / ACETATE ION / Cadmium-specific carbonic anhydrase
Function and homology information
Biological speciesThalassiosira weissflogii (Diatom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.2Aug 30, 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 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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)23,1282
Polymers23,0691
Non-polymers591
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.308, 59.206, 79.614
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cadmium-specific carbonic anhydrase


Mass: 23069.201 Da / Num. of mol.: 1 / Fragment: Domain 1, CDCA1-R1
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsRELATIVE TO THE ORIGINAL COORDINATES THE ACETATE AND WATER MOLECULE NUMBERING HAS BEEN OFFSET BY ...RELATIVE TO THE ORIGINAL COORDINATES THE ACETATE 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: 2.37 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.5 M NaH2PO4, 1.4 M K2HPO4, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 19, 2007
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. all: 39051 / Num. obs: 39051 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 6.1 % / Biso Wilson estimate: 14.3 Å2 / Rsym value: 0.075
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 2.5 % / Rsym value: 0.363 / % possible all: 90.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CDCA1-R1 cadmium bound form, PDB entry 3BOH

3boh


Resolution: 1.45→33.04 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1179673.88 / 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
Rfree0.209 1945 5 %RANDOM
Rwork0.182 ---
all0.184 38955 --
obs0.184 38955 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.9868 Å2 / ksol: 0.385679 e/Å3
Displacement parametersBiso mean: 16.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.59 Å20 Å20 Å2
2--0.46 Å20 Å2
3---2.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.45→33.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1589 0 4 230 1823
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
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_it2.42.5
X-RAY DIFFRACTIONc_mcangle_it3.323
X-RAY DIFFRACTIONc_scbond_it5.413
X-RAY DIFFRACTIONc_scangle_it6.863.5
LS refinement shellResolution: 1.45→1.54 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 312 5.2 %
Rwork0.246 5637 -
obs--91.7 %
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 DIFFRACTION4acy_xplor.par

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