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- PDB-3f7b: Crystal Structure of soluble domain of CA4 in complex with small ... -

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Basic information

Entry
Database: PDB / ID: 3f7b
TitleCrystal Structure of soluble domain of CA4 in complex with small molecule.
ComponentsCarbonic anhydrase 4
KeywordsLYASE / Structure-based drug design. Small molecule complex. CO-CRYSTAL. / Cell membrane / Disease mutation / Glycoprotein / GPI-anchor / Lipoprotein / Membrane / Metal-binding / Retinitis pigmentosa / Sensory transduction / Vision / Zinc
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-AG5 / Carbonic anhydrase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGreasley, S.E. / Ferre, R.A.A. / Pauly, T.A. / Paz, R.
CitationJournal: Bioorg.Med.Chem. / Year: 2010
Title: Thioether benzenesulfonamide inhibitors of carbonic anhydrases II and IV: structure-based drug design, synthesis, and biological evaluation.
Authors: Vernier, W. / Chong, W. / Rewolinski, D. / Greasley, S. / Pauly, T. / Shaw, M. / Dinh, D. / Ferre, R.A. / Nukui, S. / Ornelas, M. / Reyner, E.
History
DepositionNov 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 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 / struct_conn / 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_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 4
B: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6876
Polymers60,7292
Non-polymers9584
Water4,738263
1
A: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8433
Polymers30,3641
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Carbonic anhydrase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8433
Polymers30,3641
Non-polymers4792
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)125.910, 128.556, 46.365
Angle α, β, γ (deg.)90.00, 99.88, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-491-

HOH

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Components

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


Mass: 30364.473 Da / Num. of mol.: 2 / Fragment: Soluble Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA4 / Production host: Escherichia coli (E. coli) / References: UniProt: P22748, 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-AG5 / N-(2-phenylethyl)-2-(phenylsulfanyl)-5-sulfamoylpyridine-3-carboxamide


Mass: 413.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H19N3O3S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 20% PEG 3350, 0.1M Na Acetate, 0.32M Ammonium sulfate , pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 21, 2005 / Details: mirrors
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.05→19.68 Å / Num. obs: 41673 / % possible obs: 91.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 2.56 % / Biso Wilson estimate: 33.2 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 18.6
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.323 / Mean I/σ(I) obs: 2.38 / Num. unique all: 4299 / % possible all: 94.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.4.0073refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZNC

1znc


Resolution: 2.05→19.68 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.915 / SU ML: 0.108 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 1 / ESU R: 0.18 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25197 2094 5 %RANDOM
Rwork0.19062 ---
all0.2091 39564 --
obs0.19368 39564 91.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.158 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20.69 Å2
2---0.61 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4002 0 58 263 4323
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0224156
X-RAY DIFFRACTIONr_angle_refined_deg2.0721.9685620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2875493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.50125186
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.2815719
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.2681515
X-RAY DIFFRACTIONr_chiral_restr0.1710.2608
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213109
X-RAY DIFFRACTIONr_mcbond_it1.3711.52510
X-RAY DIFFRACTIONr_mcangle_it2.37224050
X-RAY DIFFRACTIONr_scbond_it3.67331646
X-RAY DIFFRACTIONr_scangle_it5.7414.51570
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 147 -
Rwork0.285 3045 -
obs--94.66 %

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