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- PDB-5ipz: Crystal structure of human carbonic anhydrase isozyme IV with 5-(... -

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Basic information

Entry
Database: PDB / ID: 5ipz
TitleCrystal structure of human carbonic anhydrase isozyme IV with 5-(2-amino-1,3-thiazol-4-yl)-2-chlorobenzenesulfonamide
ComponentsCarbonic anhydrase 4
KeywordsLYASE / drug design / carbonic anhydrase / benzenesulfonamide / metal-binding / lyase-lyase inhibitor complex
Function / homology
Function and homology information


bicarbonate transport / transport vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment / rough endoplasmic reticulum / secretory granule membrane / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / brush border membrane / trans-Golgi network ...bicarbonate transport / transport vesicle membrane / endoplasmic reticulum-Golgi intermediate compartment / rough endoplasmic reticulum / secretory granule membrane / Reversible hydration of carbon dioxide / carbonic anhydrase / carbonate dehydratase activity / brush border membrane / trans-Golgi network / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / one-carbon metabolic process / apical plasma membrane / external side of plasma membrane / perinuclear region of cytoplasm / Golgi apparatus / cell surface / extracellular exosome / zinc ion binding / membrane / plasma membrane
Similarity search - Function
Carbonic anhydrase, CA4/CA15 / 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. ...Carbonic anhydrase, CA4/CA15 / 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-6CC / Carbonic anhydrase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsSmirnov, A. / Manakova, E. / Grazulis, S.
CitationJournal: Eur. Biophys. J. / Year: 2018
Title: Intrinsic thermodynamics of high affinity inhibitor binding to recombinant human carbonic anhydrase IV.
Authors: Mickeviciute, A. / Timm, D.D. / Gedgaudas, M. / Linkuviene, V. / Chen, Z. / Waheed, A. / Michailoviene, V. / Zubriene, A. / Smirnov, A. / Capkauskaite, E. / Baranauskiene, L. / Jachno, J. / ...Authors: Mickeviciute, A. / Timm, D.D. / Gedgaudas, M. / Linkuviene, V. / Chen, Z. / Waheed, A. / Michailoviene, V. / Zubriene, A. / Smirnov, A. / Capkauskaite, E. / Baranauskiene, L. / Jachno, J. / Revuckiene, J. / Manakova, E. / Grazulis, S. / Matuliene, J. / Di Cera, E. / Sly, W.S. / Matulis, D.
History
DepositionMar 10, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jul 11, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 10, 2024Group: 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
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_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
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 4
B: Carbonic anhydrase 4
C: Carbonic anhydrase 4
D: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,11411
Polymers121,9834
Non-polymers1,1317
Water2,162120
1
A: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8513
Polymers30,4961
Non-polymers3552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8513
Polymers30,4961
Non-polymers3552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8513
Polymers30,4961
Non-polymers3552
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5612
Polymers30,4961
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.694, 256.408, 48.551
Angle α, β, γ (deg.)90.000, 117.340, 90.000
Int Tables number4
Space group name H-MP1211
Detailsbiological unit is the same as asym.

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Components

#1: Protein
Carbonic anhydrase 4 / Carbonate dehydratase IV / Carbonic anhydrase IV / CA-IV


Mass: 30495.668 Da / Num. of mol.: 4 / Fragment: UNP residues 19-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA4 / Plasmid: pET21a / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): Origami B (DE3) / References: UniProt: P22748, carbonic anhydrase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Fragment: 5-(2-amino-1,3-thiazol-4-yl)-2-chlorobenzenesulfonamide
Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-6CC / 5-(2-amino-1,3-thiazol-4-yl)-2-chlorobenzene-1-sulfonamide


Mass: 289.762 Da / Num. of mol.: 3 / Fragment: Zn / Source method: obtained synthetically / Formula: C9H8ClN3O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.21 Å3/Da / Density % sol: 43.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Crystallization buffer was 0.2 M ammonium sulfate, 0.1 M sodium MES (pH 6.5) and 20% PEG MME 2,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.826606 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.826606 Å / Relative weight: 1
ReflectionResolution: 2.1→43.129 Å / Num. all: 51979 / Num. obs: 51979 / % possible obs: 85 % / Redundancy: 2.8 % / Rpim(I) all: 0.041 / Rrim(I) all: 0.074 / Rsym value: 0.049 / Net I/av σ(I): 7.455 / Net I/σ(I): 10.5 / Num. measured all: 147290
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.212.80.4171.7177
2.21-2.352.70.3162.3182
2.35-2.512.70.2243.2185.6
2.51-2.712.70.1584.5187.2
2.71-2.972.80.1056.4188.9
2.97-3.322.80.0649.6185.8
3.32-3.8330.04412.4189
3.83-4.73.10.03414.8189
4.7-6.6430.02916188.9
6.64-43.1330.0289.7181.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F7B

3f7b


Resolution: 2.1→43.129 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.903 / SU R Cruickshank DPI: 0.414 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.414 / ESU R Free: 0.298
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.306 5105 9.8 %RANDOM
Rwork0.225 ---
obs0.233 51926 84.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 125.97 Å2 / Biso mean: 50.333 Å2 / Biso min: 17.19 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0.98 Å2
2---0.25 Å20 Å2
3----0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.1→43.129 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8225 0 55 120 8400
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.028508
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.96511548
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.51351023
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.5525.063395
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.482151524
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2141532
X-RAY DIFFRACTIONr_chiral_restr0.1180.21239
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216438
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 336 -
Rwork0.274 3094 -
all-3430 -
obs--77.04 %

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