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- PDB-3mwo: Human carbonic anhydrase II in a doubled monoclinic cell: a re-de... -

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Basic information

Entry
Database: PDB / ID: 3mwo
TitleHuman carbonic anhydrase II in a doubled monoclinic cell: a re-determination
ComponentsCarbonic anhydrase 2
KeywordsLYASE / DOUBLED UNIT CELL / pseudosymmetry / Translational NCS
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 / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / regulation of chloride transport / arylesterase activity / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / regulation of intracellular pH / 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 / one-carbon metabolic process / 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
Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4 Å
AuthorsRobbins, A.H. / McKenna, R.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2010
Title: Emerging from pseudo-symmetry: the redetermination of human carbonic anhydrase II in monoclinic P2(1) with a doubled a axis.
Authors: Robbins, A.H. / Domsic, J.F. / Agbandje-McKenna, M. / McKenna, R.
History
DepositionMay 6, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionJun 9, 2010ID: 3KS1
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Apr 20, 2016Group: Refinement description
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Sep 6, 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 / 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_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_label_asym_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_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_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_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 2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,7094
Polymers58,5782
Non-polymers1312
Water13,421745
1
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3542
Polymers29,2891
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3542
Polymers29,2891
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.981, 41.057, 73.586
Angle α, β, γ (deg.)90.000, 109.330, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 29289.062 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2, HCA2 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 745 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUE NUMBERING FOLLOWS THAT REPORTED FOR THE HUMAN CARBONIC ANHYDRASE ISOFORM II, PDB CODE 1CA2.

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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: 2.04 Å3/Da / Density % sol: 39.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 50 mM Tris, 1.2 M sodium citrate, 5 ul + 5 ul droplet, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9782 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 22, 2009 / Details: mirrors
RadiationMonochromator: ASYMMETRIC CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9782 Å / Relative weight: 1
ReflectionResolution: 1.4→20 Å / Num. all: 90618 / Num. obs: 90618 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Χ2: 1.083 / Net I/σ(I): 15.1
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 3 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 6.2 / Num. unique all: 8883 / Rsym value: 0.194 / Χ2: 1.081 / % possible all: 95.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.6.1_348refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
RefinementStarting model: 3KS1

3ks1
PDB Unreleased entry


Resolution: 1.4→18.279 Å / Occupancy max: 1 / Occupancy min: 0.3 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 0.6 / σ(I): 0 / Stereochemistry target values: ML
Details: 3KS1, chain B (altloc B removed), model translated x'=x-1/4 and re-refined
RfactorNum. reflection% reflectionSelection details
Rfree0.184 4581 5.08 %RANDOM
Rwork0.166 ---
all0.167 90110 --
obs0.167 90110 96.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.7 Å2 / ksol: 0.475 e/Å3
Displacement parametersBiso max: 72.97 Å2 / Biso mean: 16.011 Å2 / Biso min: 3.76 Å2
Baniso -1Baniso -2Baniso -3
1-1.507 Å2-0 Å2-0.002 Å2
2---0.477 Å2-0 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 1.4→18.279 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4098 0 2 745 4845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094343
X-RAY DIFFRACTIONf_angle_d1.2575925
X-RAY DIFFRACTIONf_chiral_restr0.076622
X-RAY DIFFRACTIONf_plane_restr0.007771
X-RAY DIFFRACTIONf_dihedral_angle_d11.981623
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.4160.2431510.1982710286192
1.416-1.4330.2161500.1912800295096
1.433-1.450.1891400.1842826296695
1.45-1.4680.2121460.1832821296796
1.468-1.4880.1961770.1752773295096
1.488-1.5080.1981490.1752837298696
1.508-1.530.2041640.1842835299996
1.53-1.5520.211500.172811296196
1.552-1.5770.2051450.1642850299596
1.577-1.6020.1841450.1592830297597
1.602-1.630.1871520.1622877302997
1.63-1.660.2021210.1622859298097
1.66-1.6920.2221640.1632836300097
1.692-1.7260.1781550.1582899305497
1.726-1.7640.1731470.1562846299397
1.764-1.8050.2151530.1572858301197
1.805-1.850.1721710.1552839301097
1.85-1.90.1531610.1562897305897
1.9-1.9560.1651480.1512905305397
1.956-2.0190.1781520.1542862301498
2.019-2.0910.1561640.1492886305098
2.091-2.1740.1751440.1472924306897
2.174-2.2730.1891470.152899304697
2.273-2.3920.1721520.1462910306298
2.392-2.5420.1721560.1592910306698
2.542-2.7380.1851700.1642911308198
2.738-3.0120.1781720.1642883305598
3.012-3.4450.1761330.162959309298
3.445-4.3310.1731610.1552845300695
4.331-18.2810.1741410.2192631277285
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5207-0.01620.00120.4946-0.1280.6131-0.012-0.0325-0.0102-0.07790.01040.01820.0395-0.01240.00270.039-0.00450.00050.03190.00040.03259.4951.38515.831
20.6026-0.083-0.06960.46350.00930.4402-0.0117-0.04810.0032-0.0010.0199-0.02270.0132-0.0053-0.00860.0356-0.0007-0.00330.0355-0.00410.042751.6291.39515.713
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 263:781 ) OR ( CHAIN B AND RESID 126:780 )A263 - 781
2X-RAY DIFFRACTION1( CHAIN A AND RESID 263:781 ) OR ( CHAIN B AND RESID 126:780 )B126 - 780
3X-RAY DIFFRACTION2( CHAIN B AND RESID 4:125 )B4 - 125

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