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- PDB-1ekj: THE X-RAY CRYSTALLOGRAPHIC STRUCTURE OF BETA CARBONIC ANHYDRASE F... -

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Basic information

Entry
Database: PDB / ID: 1ekj
TitleTHE X-RAY CRYSTALLOGRAPHIC STRUCTURE OF BETA CARBONIC ANHYDRASE FROM THE C3 DICOT PISUM SATIVUM
ComponentsBETA-CARBONIC ANHYDRASE
KeywordsLYASE / ROSSMAN FOLD DOMAIN / STRAND EXCHANGE
Function / homology
Function and homology information


carbon utilization / chloroplast stroma / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding
Similarity search - Function
Beta carbonic anhydrases, cladeB / 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 ...Beta carbonic anhydrases, cladeB / 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
ACETATE ION / AZIDE ION / CITRIC ACID / COPPER (II) ION / Carbonic anhydrase, chloroplastic
Similarity search - Component
Biological speciesPisum sativum (garden pea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.93 Å
AuthorsKimber, M.S. / Pai, E.F.
Citation
Journal: EMBO J. / Year: 2000
Title: The active site architecture of Pisum sativum beta-carbonic anhydrase is a mirror image of that of alpha-carbonic anhydrases.
Authors: Kimber, M.S. / Pai, E.F.
#1: Journal: To be Published
Title: Beta-Carbonic Anhydrase from Pisum Sativum: Crystallisation and Preliminary X-Ray Analysis
Authors: Kimber, M.S. / Coleman, J.R. / Pai, E.F.
History
DepositionMar 8, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 1, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BETA-CARBONIC ANHYDRASE
B: BETA-CARBONIC ANHYDRASE
C: BETA-CARBONIC ANHYDRASE
D: BETA-CARBONIC ANHYDRASE
E: BETA-CARBONIC ANHYDRASE
F: BETA-CARBONIC ANHYDRASE
G: BETA-CARBONIC ANHYDRASE
H: BETA-CARBONIC ANHYDRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,93946
Polymers191,7388
Non-polymers2,20138
Water14,610811
1
A: BETA-CARBONIC ANHYDRASE
B: BETA-CARBONIC ANHYDRASE
C: BETA-CARBONIC ANHYDRASE
D: BETA-CARBONIC ANHYDRASE
hetero molecules

A: BETA-CARBONIC ANHYDRASE
B: BETA-CARBONIC ANHYDRASE
C: BETA-CARBONIC ANHYDRASE
D: BETA-CARBONIC ANHYDRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,07246
Polymers191,7388
Non-polymers2,33438
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area38930 Å2
ΔGint-217.5 kcal/mol
Surface area61470 Å2
MethodPISA
2
E: BETA-CARBONIC ANHYDRASE
F: BETA-CARBONIC ANHYDRASE
G: BETA-CARBONIC ANHYDRASE
H: BETA-CARBONIC ANHYDRASE
hetero molecules

E: BETA-CARBONIC ANHYDRASE
F: BETA-CARBONIC ANHYDRASE
G: BETA-CARBONIC ANHYDRASE
H: BETA-CARBONIC ANHYDRASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,80646
Polymers191,7388
Non-polymers2,06838
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655-x+3/2,-y+1/2,z1
Buried area38950 Å2
ΔGint-216.1 kcal/mol
Surface area62340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.909, 143.318, 202.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
BETA-CARBONIC ANHYDRASE


Mass: 23967.291 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: NUCLEAR ENCODED / Organ: LEAF / References: UniProt: P17067, carbonic anhydrase

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Non-polymers , 8 types, 849 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: N3
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#8: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 811 / 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: 2.58 Å3/Da / Density % sol: 52.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: 16% PEG 4000, 0.05 M DITHIOTHREITOL, 0.4 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 %PEG4000 1reservoir
2400 mMammonium acetate1reservoir
350 mMdithiothreitol1reservoir
4100 mMsodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Type: APS / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→40 Å / Num. obs: 138484 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13
Reflection shellHighest resolution: 1.93 Å / Rmerge(I) obs: 0.277 / % possible all: 78.5
Reflection
*PLUS
Num. measured all: 779081
Reflection shell
*PLUS
% possible obs: 78.5 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.93→40 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: TORSION ANGLE ANNEALING REFINEMENT TO MAXIMIMUM LIKELIHOOD TARGETS, FOLLOWED BY INDIVIDUAL TEMPERATURE FACTOR REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1298 1 %RANDOM
Rwork0.229 ---
obs0.229 130054 87.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.75 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 45.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.16 Å20 Å20 Å2
2--11 Å20 Å2
3----13.17 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 1.93→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13162 0 97 811 14070
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
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_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.81.5
X-RAY DIFFRACTIONc_mcangle_it2.582
X-RAY DIFFRACTIONc_scbond_it2.572
X-RAY DIFFRACTIONc_scangle_it3.462.5
LS refinement shellResolution: 1.93→2.05 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.324 171 1 %
Rwork0.306 17133 -
obs--70.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP_ZN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ACETATE.PARAMACETATE.TOP
X-RAY DIFFRACTION4ION.PARAMION_NEW.TOP
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.09

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