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- PDB-1ddz: X-RAY STRUCTURE OF A BETA-CARBONIC ANHYDRASE FROM THE RED ALGA, P... -

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Basic information

Entry
Database: PDB / ID: 1ddz
TitleX-RAY STRUCTURE OF A BETA-CARBONIC ANHYDRASE FROM THE RED ALGA, PORPHYRIDIUM PURPUREUM R-1
ComponentsCARBONIC ANHYDRASE
KeywordsLYASE / ALPHA-BETA-ALPHA
Function / homology
Function and homology information


carbon utilization / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Prokaryotic-type carbonic anhydrases signature 1. / Prokaryotic-type carbonic anhydrases signature 2. / Carbonic anhydrase, prokaryotic-like, conserved site / Beta-carbonic Anhydrase; Chain A / Carbonic anhydrase / Carbonic anhydrase / Carbonic anhydrase superfamily / Carbonic anhydrase / Carbonic anhydrase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPorphyridium purpureum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsMitsuhashi, S. / Mizushima, T. / Yamashita, E. / Miyachi, S. / Tsukihara, T.
CitationJournal: J.Biol.Chem. / Year: 2000
Title: X-ray structure of beta-carbonic anhydrase from the red alga, Porphyridium purpureum, reveals a novel catalytic site for CO(2) hydration.
Authors: Mitsuhashi, S. / Mizushima, T. / Yamashita, E. / Yamamoto, M. / Kumasaka, T. / Moriyama, H. / Ueki, T. / Miyachi, S. / Tsukihara, T.
History
DepositionNov 12, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 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_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_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.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CARBONIC ANHYDRASE
B: CARBONIC ANHYDRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2496
Polymers109,9872
Non-polymers2624
Water11,025612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-6 kcal/mol
Surface area32810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.500, 112.800, 73.200
Angle α, β, γ (deg.)90.00, 103.60, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein CARBONIC ANHYDRASE /


Mass: 54993.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyridium purpureum (eukaryote) / Variant: R-1 / Plasmid: PET16B / Production host: Escherichia coli (E. coli) / References: UniProt: Q43060, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 612 / 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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.75
Details: PEG4000, AMMONIUM SULFATE, SODIUM CACODYLATE, pH 6.75, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
220 mM1dropNaCl
320 mMTris-HCl1drop
424 %PEG40001reservoir
5300 mMammonium sulfate1reservoir
650 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→60 Å / Num. all: 326527 / Num. obs: 50489 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 16.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.227 / % possible all: 99.8
Reflection
*PLUS
Num. measured all: 326527
Reflection shell
*PLUS
Num. possible: 27202 / Num. unique obs: 5016 / Mean I/σ(I) obs: 4.5

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Processing

Software
NameVersionClassification
SHARPphasing
X-PLOR3.843refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.2→10 Å / σ(F): 2 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.274 2524 RANDOM
Rwork0.208 --
obs0.208 --
all-49836 -
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7484 0 4 612 8100
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it

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