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- PDB-6h6s: Sad phasing on nickel-substituted human carbonic anhydrase II -

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Basic information

Entry
Database: PDB / ID: 6h6s
TitleSad phasing on nickel-substituted human carbonic anhydrase II
ComponentsCarbonic anhydrase 2
KeywordsHYDROLASE / CAII / nickel / SAD
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase activity / cyanamide hydratase / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / regulation of intracellular pH / positive regulation of synaptic transmission, GABAergic / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
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 ...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
NICKEL (II) ION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.45 Å
AuthorsCalderone, V. / Fragai, M. / Silva, J.P. / Luchinat, C. / Ravera, E. / Geraldes, C.F.G.C. / Macedo, A.L. / Cerofolini, L. / Giuntini, S.
CitationJournal: J. Biol. Inorg. Chem. / Year: 2019
Title: Non-crystallographic symmetry in proteins: Jahn-Teller-like and Butterfly-like effects?
Authors: Silva, J.M. / Giuntini, S. / Cerofolini, L. / Geraldes, C.F.G.C. / Macedo, A.L. / Ravera, E. / Fragai, M. / Luchinat, C. / Calderone, V.
History
DepositionJul 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 9, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Aug 21, 2019Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / struct_conn
Revision 1.3Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.4May 15, 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
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5506
Polymers58,3162
Non-polymers2354
Water11,872659
1
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2753
Polymers29,1581
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2753
Polymers29,1581
Non-polymers1172
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.480, 41.180, 84.040
Angle α, β, γ (deg.)90.00, 109.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29157.863 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / 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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 100 mM HEPES, 2.9 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.48306 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.48306 Å / Relative weight: 1
ReflectionResolution: 1.45→45.34 Å / Num. obs: 154486 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Net I/σ(I): 12.6
Reflection shellResolution: 1.45→1.54 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.29 / Num. unique obs: 22243 / CC1/2: 0.93 / % possible all: 83.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
XDSdata reduction
XSCALEdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.45→45.34 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.967 / SU B: 2.602 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.076 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20365 4047 5 %RANDOM
Rwork0.14973 ---
obs0.15243 76886 95.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.416 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å2-0 Å20.06 Å2
2---0.6 Å2-0 Å2
3---0.22 Å2
Refinement stepCycle: 1 / Resolution: 1.45→45.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4116 0 4 672 4792
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0144240
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173784
X-RAY DIFFRACTIONr_angle_refined_deg1.9011.655752
X-RAY DIFFRACTIONr_angle_other_deg1.0771.6458890
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3345514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.49923.679212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.74515706
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9431514
X-RAY DIFFRACTIONr_chiral_restr0.1020.2514
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02810
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1191.3092062
X-RAY DIFFRACTIONr_mcbond_other2.1151.3072061
X-RAY DIFFRACTIONr_mcangle_it2.4911.9652574
X-RAY DIFFRACTIONr_mcangle_other2.4931.9672575
X-RAY DIFFRACTIONr_scbond_it3.5411.6552178
X-RAY DIFFRACTIONr_scbond_other3.541.6582179
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8682.3393179
X-RAY DIFFRACTIONr_long_range_B_refined4.21217.5074907
X-RAY DIFFRACTIONr_long_range_B_other4.0516.7174761
X-RAY DIFFRACTIONr_rigid_bond_restr3.9538024
X-RAY DIFFRACTIONr_sphericity_free22.1245429
X-RAY DIFFRACTIONr_sphericity_bonded11.8858147
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 232 -
Rwork0.223 4407 -
obs--75.3 %

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