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- PDB-9lr6: Zn-Carbonic Anhydrase II complexed with 3NPA at RT -

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Basic information

Entry
Database: PDB / ID: 9lr6
TitleZn-Carbonic Anhydrase II complexed with 3NPA at RT
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 / cyanamide hydratase activity / 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 / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / morphogenesis of an epithelium / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / 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, 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
2-(3-NITROPHENYL)ACETIC ACID / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsKim, C.U. / Kim, J.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Samsung Science and Technology FoundationSSTF-BA1702-04 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
DepositionJan 29, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5363
Polymers29,2891
Non-polymers2472
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-33 kcal/mol
Surface area11960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.889, 41.795, 72.869
Angle α, β, γ (deg.)90.000, 104.633, 90.000
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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MNP / 2-(3-NITROPHENYL)ACETIC ACID


Mass: 181.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.16 Å3/Da / Density % sol: 42.99 %
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: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.25→30 Å / Num. obs: 69133 / % possible obs: 99.7 % / Redundancy: 4.2 % / CC1/2: 0.98 / CC star: 0.995 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.055 / Rrim(I) all: 0.112 / Net I/σ(I): 13.8
Reflection shellResolution: 1.25→1.27 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3457 / CC1/2: 0.81 / CC star: 0.946 / Rpim(I) all: 0.27 / Rrim(I) all: 0.553 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0430phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→21.434 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.228 / SU ML: 0.024 / Cross valid method: FREE R-VALUE / ESU R: 0.036 / ESU R Free: 0.035
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1442 3500 5.065 %
Rwork0.1225 65601 -
all0.124 --
obs-69101 99.713 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 14.422 Å2
Baniso -1Baniso -2Baniso -3
1-0.113 Å20 Å2-0.072 Å2
2--0.116 Å20 Å2
3----0.169 Å2
Refinement stepCycle: LAST / Resolution: 1.25→21.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 14 242 2305
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122228
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162040
X-RAY DIFFRACTIONr_angle_refined_deg1.9341.8173046
X-RAY DIFFRACTIONr_angle_other_deg0.7321.7814748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7735282
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.66858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.24710371
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.99910105
X-RAY DIFFRACTIONr_chiral_restr0.1330.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022670
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02500
X-RAY DIFFRACTIONr_nbd_refined0.1930.2348
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.21699
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21007
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21103
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2116
X-RAY DIFFRACTIONr_metal_ion_refined0.060.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2440.210
X-RAY DIFFRACTIONr_nbd_other0.2020.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1430.213
X-RAY DIFFRACTIONr_mcbond_it4.7011.2281080
X-RAY DIFFRACTIONr_mcbond_other4.6751.2271080
X-RAY DIFFRACTIONr_mcangle_it6.4552.2181366
X-RAY DIFFRACTIONr_mcangle_other6.4632.221367
X-RAY DIFFRACTIONr_scbond_it6.9311.5831148
X-RAY DIFFRACTIONr_scbond_other6.9281.5841149
X-RAY DIFFRACTIONr_scangle_it9.8572.7151676
X-RAY DIFFRACTIONr_scangle_other9.8552.7151677
X-RAY DIFFRACTIONr_lrange_it16.3615.0942375
X-RAY DIFFRACTIONr_lrange_other15.81313.5012335
X-RAY DIFFRACTIONr_rigid_bond_restr5.06534268
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.25-1.2820.1942470.18747870.18850350.9790.9899.98010.17
1.282-1.3170.1682390.15147170.15249560.9820.9851000.132
1.317-1.3550.152370.13445980.13548350.9860.9881000.117
1.355-1.3970.1562480.12744380.12846860.9820.9891000.111
1.397-1.4430.1422160.11343020.11445190.9870.99199.97790.099
1.443-1.4930.1422040.10542300.10644360.9870.99399.95490.092
1.493-1.5490.1292100.10340030.10442140.9880.99399.97630.093
1.549-1.6120.1261840.09738940.09840820.9890.99499.9020.09
1.612-1.6830.1312090.09936900.10139000.9890.99499.97440.094
1.683-1.7650.1291980.10135680.10237680.990.99499.94690.099
1.765-1.860.1371970.133670.10235710.9890.99499.8040.101
1.86-1.9710.1262120.10231570.10333730.990.99399.88140.105
1.971-2.1060.1431630.1130080.11131790.9870.99399.74840.117
2.106-2.2730.1381560.11628190.11729880.9870.99199.56490.127
2.273-2.4870.141250.12525980.12627340.9890.99199.59770.142
2.487-2.7760.1861080.1423760.14224990.9790.98899.39980.165
2.776-3.1970.1681200.14220710.14322080.9820.98799.23010.172
3.197-3.8940.1521040.13117710.13218940.9840.98998.99680.168
3.894-5.4180.121900.11913570.11914820.9910.99297.63830.161
5.418-21.4340.155330.1678250.1678940.9830.98195.97320.233

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