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- PDB-9kh8: Co-Carbonic Anhydrase II complexed with 3NPA before UV at 100 K -

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Basic information

Entry
Database: PDB / ID: 9kh8
TitleCo-Carbonic Anhydrase II complexed with 3NPA before UV at 100 K
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / carbonic anhydrase / enzyme mechanism / metalloenzymes
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, 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
Similarity search - Domain/homology
BICARBONATE ION / : / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsKim, C.U. / Kim, J.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other privateSSTF-BA1702-04 (Samsung Science and Technology Foundation) Korea, Republic Of
CitationJournal: To Be Published
Title: Temperature series of human Carbonic Anhydrase II with photolysis of caged CO2
Authors: Kim, C.U. / Kim, J.K.
History
DepositionNov 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4093
Polymers29,2891
Non-polymers1202
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.191, 41.220, 72.260
Angle α, β, γ (deg.)90.00, 104.25, 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: 29289.062 Da / Num. of mol.: 1
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-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.08 Å3/Da / Density % sol: 40.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.3 M sodium citrate, 50 mM Tris-HCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 2, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 74142 / % possible obs: 98.2 % / Redundancy: 3.7 % / CC1/2: 0.978 / CC star: 0.995 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.06 / Rrim(I) all: 0.116 / Net I/σ(I): 12.8
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.337 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 3614 / CC1/2: 0.881 / CC star: 0.968 / Rpim(I) all: 0.203 / Rrim(I) all: 0.394 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0135phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→30 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.124 / SU ML: 0.023 / Cross valid method: FREE R-VALUE / ESU R: 0.037 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16438 3802 5.1 %RANDOM
Rwork0.13412 ---
obs0.1357 70276 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.311 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å2-0.17 Å2
2--0.14 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: 1 / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 5 287 2341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0192234
X-RAY DIFFRACTIONr_bond_other_d0.0030.022070
X-RAY DIFFRACTIONr_angle_refined_deg2.5441.9483047
X-RAY DIFFRACTIONr_angle_other_deg1.30734812
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7435285
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.96825106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2615374
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.275157
X-RAY DIFFRACTIONr_chiral_restr0.1790.2318
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212580
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02515
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_it2.4491.1671083
X-RAY DIFFRACTIONr_mcbond_other2.3461.1621082
X-RAY DIFFRACTIONr_mcangle_it3.0921.7571369
X-RAY DIFFRACTIONr_mcangle_other3.1311.7611370
X-RAY DIFFRACTIONr_scbond_it4.5531.4931151
X-RAY DIFFRACTIONr_scbond_other4.5511.4921152
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2462.1031672
X-RAY DIFFRACTIONr_long_range_B_refined7.54211.5352737
X-RAY DIFFRACTIONr_long_range_B_other6.73510.732596
X-RAY DIFFRACTIONr_rigid_bond_restr5.73734304
X-RAY DIFFRACTIONr_sphericity_free45.78565
X-RAY DIFFRACTIONr_sphericity_bonded16.38554447
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.201 254 -
Rwork0.183 5084 -
obs--96.21 %

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