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- PDB-3da2: X-ray structure of human carbonic anhydrase 13 in complex with in... -

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Basic information

Entry
Database: PDB / ID: 3da2
TitleX-ray structure of human carbonic anhydrase 13 in complex with inhibitor
ComponentsCarbonic anhydrase 13
KeywordsLYASE / CARBONIC ANHYDRASE / SULFONAMIDE / SGC / Structural Genomics / Structural Genomics Consortium / Metal-binding
Function / homology
Function and homology information


Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / one-carbon metabolic process / myelin sheath / intracellular membrane-bounded organelle / zinc ion binding / 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
Chem-4MD / Carbonic anhydrase 13
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPilka, E.S. / Picaud, S.S. / Yue, W.W. / King, O.N.F. / Bray, J.E. / Filippakopoulos, P. / Roos, A.K. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. ...Pilka, E.S. / Picaud, S.S. / Yue, W.W. / King, O.N.F. / Bray, J.E. / Filippakopoulos, P. / Roos, A.K. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Wikstrom, M. / Edwards, A.M. / Bountra, C. / Oppermann, U. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: X-ray structure of human carbonic anhydrase 13 in complex with inhibitor.
Authors: Pilka, E.S. / Picaud, S.S. / Yue, W.W. / King, O.N.F. / Bray, J.E. / Filippakopoulos, P. / Roos, A.K. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Wikstrom, M. / Edwards, A.M. / ...Authors: Pilka, E.S. / Picaud, S.S. / Yue, W.W. / King, O.N.F. / Bray, J.E. / Filippakopoulos, P. / Roos, A.K. / Pike, A.C.W. / von Delft, F. / Arrowsmith, C.H. / Wikstrom, M. / Edwards, A.M. / Bountra, C. / Oppermann, U.
History
DepositionMay 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 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_conn / 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_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _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

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 13
B: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8148
Polymers58,8622
Non-polymers9516
Water7,837435
1
A: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8713
Polymers29,4311
Non-polymers4402
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9425
Polymers29,4311
Non-polymers5114
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)153.637, 45.138, 87.938
Angle α, β, γ (deg.)90.00, 116.28, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Carbonic anhydrase 13 / Carbonic anhydrase XIII / Carbonate dehydratase XIII / CA-XIII


Mass: 29431.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA13 / Plasmid: pNIC-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA / References: UniProt: Q8N1Q1, carbonic anhydrase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-4MD / N-(4-chlorobenzyl)-N-methylbenzene-1,4-disulfonamide


Mass: 374.863 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15ClN2O4S2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 47.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 20% PEG 3350, 0.2M (NH4)2H(citrate), pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00001 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 10, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.05→43.52 Å / Num. all: 34326 / Num. obs: 32583 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.096 / Rsym value: 0.057 / Net I/σ(I): 11
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.621 / Mean I/σ(I) obs: 2.3 / Num. unique all: 4941 / Rsym value: 0.372 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0066refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1AZM,1ZH9,1FLJ

1azm

1zh9

1flj


Resolution: 2.05→43 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.16 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22063 1734 5.1 %RANDOM
Rwork0.15903 ---
all0.16224 32583 --
obs0.16224 32583 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.183 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å20 Å2-0.18 Å2
2--0.77 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.05→43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4063 0 50 435 4548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214267
X-RAY DIFFRACTIONr_bond_other_d0.0010.022840
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9555834
X-RAY DIFFRACTIONr_angle_other_deg0.9183.0016912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg14.1675525
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.48124.149188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.48815654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5021518
X-RAY DIFFRACTIONr_chiral_restr0.0890.2628
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0214778
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02846
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_it2.17632621
X-RAY DIFFRACTIONr_mcbond_other0.62831042
X-RAY DIFFRACTIONr_mcangle_it3.41154247
X-RAY DIFFRACTIONr_scbond_it5.49971646
X-RAY DIFFRACTIONr_scangle_it7.239111587
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 121 -
Rwork0.205 2359 -
obs--99.92 %
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)
118.60813.9647-4.08287.96890.06361.01810.0414-0.45260.51280.0732-0.18660.3975-1.2646-0.13750.14510.46620.11910.02560.2214-0.00490.34925.67430.89113.767
23.8443-0.1638-0.21631.9168-0.00232.5560.10930.1659-0.17410.04-0.2882-0.02670.0299-0.10250.17880.0181-0.0465-0.03270.0508-0.016-0.03066.67210.94116.248
33.0672-0.6292-0.05571.3056-0.00623.31440.0168-0.004-0.17740.2409-0.14590.26420.0435-0.67140.12910.0531-0.06350.02610.1799-0.0390.003-3.75711.39721.428
43.8271-0.5577-0.1011.89050.20212.71660.11530.3215-0.27020.0887-0.24390.20810.1058-0.43170.12870.0217-0.04050.00710.1297-0.0601-0.02120.1559.2314.798
52.50740.6620.00042.4529-0.37722.611-0.0635-0.2553-0.45380.13860.1519-0.01140.4568-0.0983-0.08840.1187-0.0406-0.01550.05380.04610.033332.852-20.13619.639
61.91850.06950.08852.9345-0.54622.2103-0.0682-0.02090.1681-0.04630.23010.0369-0.1706-0.0624-0.16190.0474-0.03650.0250.03910.0058-0.003733.69-4.55514.951
73.6479-2.28771.51652.9722-1.18971.4562-0.2925-0.1760.40240.76780.31060.0363-0.7645-0.2812-0.0180.36050.11290.04830.1521-0.06250.05829.0465.6627.684
82.04890.26210.2872.5676-0.37582.6097-0.0814-0.17640.02230.16460.1604-0.0946-0.079-0.0061-0.07890.046-0.003200.0323-0.0058-0.027236.448-9.14420.93
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 62 - 7
2X-RAY DIFFRACTION2AA7 - 598 - 60
3X-RAY DIFFRACTION3AA60 - 18161 - 182
4X-RAY DIFFRACTION4AA182 - 261183 - 262
5X-RAY DIFFRACTION5BB6 - 457 - 46
6X-RAY DIFFRACTION6BB46 - 15547 - 156
7X-RAY DIFFRACTION7BB156 - 180157 - 181
8X-RAY DIFFRACTION8BB181 - 261182 - 262

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