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- PDB-9f2f: Carbonic anhydrase II variant with bound iron complex in space gr... -

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Basic information

Entry
Database: PDB / ID: 9f2f
TitleCarbonic anhydrase II variant with bound iron complex in space group R3 (ArPase)
ComponentsCarbonic anhydrase 2
KeywordsOXIDOREDUCTASE / artificial enzyme / metalloenzyme / peroxidase / human carbonic anhydrase
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 / 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
: / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.52 Å
AuthorsJakob, R.P. / Ward, T.R.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation180544 Switzerland
CitationJournal: Acs Catalysis / Year: 2024
Title: Directed Evolution of an Artificial Hydroxylase Based on a Thermostable Human Carbonic Anhydrase Protein
Authors: Morita, I. / Faraone, A. / Salvisberg, E. / Zhang, K. / Jakob, R.P. / Maier, T. / Ward, T.R.
History
DepositionApr 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 5, 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
B: Carbonic anhydrase 2
C: Carbonic anhydrase 2
D: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,29233
Polymers117,1364
Non-polymers4,15629
Water29,4001632
1
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3098
Polymers29,2841
Non-polymers1,0257
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3719
Polymers29,2841
Non-polymers1,0878
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3659
Polymers29,2841
Non-polymers1,0818
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2477
Polymers29,2841
Non-polymers9636
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.167, 179.167, 109.705
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein
Carbonic anhydrase 2 / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Cyanamide ...Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II / Cyanamide hydratase CA2


Mass: 29283.895 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P00918, carbonic anhydrase, cyanamide hydratase
#2: Chemical
ChemComp-A1H9O / 4,4,7,10,10-pentamethyl-3,6,8,11-tetrakis(oxidanylidene)-N-[2-(4-sulfamoylphenyl)ethyl]-2,5,7,9,12-pentazabicyclo[11.4.0]heptadeca-1(13),14,16-triene-15-carboxamide containing iron


Mass: 639.461 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C26H29FeN7O7S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1632 / 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: 2.89 Å3/Da / Density % sol: 57.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Magnesium acetate tetrahydrate, 0.1M MOPS pH 7.5, 12% w/v PEG 8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 14, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.52→44.792 Å / Num. obs: 202072 / % possible obs: 100 % / Redundancy: 21.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.042 / Net I/σ(I): 13
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 20.4 % / Rmerge(I) obs: 2.01 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 20121 / CC1/2: 0.717 / Rpim(I) all: 0.66 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.12rc1_2801: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.52→44.792 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 17.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.167 10204 5.06 %
Rwork0.1465 --
obs0.1476 201826 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.52→44.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8264 0 226 1640 10130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0168919
X-RAY DIFFRACTIONf_angle_d1.48312184
X-RAY DIFFRACTIONf_dihedral_angle_d14.4125231
X-RAY DIFFRACTIONf_chiral_restr0.0841242
X-RAY DIFFRACTIONf_plane_restr0.0111566
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.52-1.53730.28232870.24116332X-RAY DIFFRACTION100
1.5373-1.55540.2643690.22536344X-RAY DIFFRACTION99
1.5554-1.57430.23523200.21266389X-RAY DIFFRACTION100
1.5743-1.59430.22913890.21276329X-RAY DIFFRACTION100
1.5943-1.61520.28962450.22376590X-RAY DIFFRACTION100
1.6152-1.63740.2073400.17886370X-RAY DIFFRACTION100
1.6374-1.66080.2172920.18916315X-RAY DIFFRACTION100
1.6608-1.68560.23444000.18466415X-RAY DIFFRACTION100
1.6856-1.71190.19083480.17216338X-RAY DIFFRACTION100
1.7119-1.740.16993120.16416440X-RAY DIFFRACTION100
1.74-1.770.20112820.15926529X-RAY DIFFRACTION100
1.77-1.80210.17163190.15176309X-RAY DIFFRACTION100
1.8021-1.83680.20622950.15136450X-RAY DIFFRACTION100
1.8368-1.87430.17333360.14696341X-RAY DIFFRACTION100
1.8743-1.91510.16423670.15236352X-RAY DIFFRACTION100
1.9151-1.95960.17724080.14996398X-RAY DIFFRACTION100
1.9596-2.00860.16422440.15576437X-RAY DIFFRACTION100
2.0086-2.06290.18324240.15256289X-RAY DIFFRACTION100
2.0629-2.12360.18182780.14946513X-RAY DIFFRACTION100
2.1236-2.19220.16984480.14746314X-RAY DIFFRACTION100
2.1922-2.27050.16483200.14176387X-RAY DIFFRACTION100
2.2705-2.36140.18283800.14696375X-RAY DIFFRACTION100
2.3614-2.46890.15323920.1456322X-RAY DIFFRACTION100
2.4689-2.5990.18692920.14736487X-RAY DIFFRACTION100
2.599-2.76190.16114090.14126312X-RAY DIFFRACTION100
2.7619-2.97510.19014440.14366299X-RAY DIFFRACTION100
2.9751-3.27440.16782370.14036413X-RAY DIFFRACTION100
3.2744-3.7480.14982600.13776533X-RAY DIFFRACTION100
3.748-4.72120.11773840.11166357X-RAY DIFFRACTION100
4.7212-44.7920.1483830.13866343X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.64890.14590.26081.27950.08551.60060.0758-0.01320.0690.0298-0.0322-0.16140.04160.1591-0.04770.0954-0.0120.00180.1181-0.00110.118250.48321.715-1.8025
21.20180.49280.36541.3090.40031.02850.2357-0.55050.26190.5237-0.20480.20270.0905-0.5102-0.05330.4459-0.14070.03840.3612-0.0350.156636.6368-2.103121.8176
31.5030.4841-0.46491.47120.08421.41230.2453-0.03110.07060.1629-0.09670.26510.0252-0.2868-0.1230.2088-0.0638-0.00690.20610.01730.19633.5622-14.3663-1.6728
40.87460.33460.55441.46560.49911.04770.1267-0.2545-0.07630.2147-0.11420.04850.1969-0.1659-0.02140.2085-0.0709-0.00420.19220.01410.131239.2311-8.73627.4033
50.99590.63860.09081.37540.45561.07560.1126-0.15320.00680.1366-0.07120.12230.1091-0.1532-0.05070.1771-0.06040.01790.2068-0.00250.143135.8281-5.46575.6787
61.3021.3948-0.06692.1073-2.20367.3497-0.0204-0.0062-0.3494-0.3792-0.0925-0.18081.5278-0.04270.09250.4417-0.0572-0.05690.19790.03010.228639.8704-25.0546-0.123
70.4870.22770.37460.99230.36990.79660.1385-0.1825-0.1430.168-0.13560.03620.2724-0.1047-0.02410.2809-0.1011-0.02110.2070.01370.170635.6376-18.27162.5742
80.76230.19970.22381.07590.31920.96350.1457-0.1881-0.08060.237-0.1225-0.01520.1535-0.0883-0.04490.1922-0.0558-0.01250.20140.0070.140541.959-4.36679.7319
91.94740.3249-0.39222.4127-1.07854.22360.03430.2576-0.2509-0.32830.0448-0.22370.58430.2163-0.09890.3127-0.0024-0.02360.2008-0.03050.240649.619-19.9835-6.14
101.05070.6497-0.21951.3398-0.6120.29250.2019-0.1620.02740.2058-0.0621-0.1747-0.0635-0.0002-0.05190.1792-0.0284-0.04560.19320.00060.14948.8444-2.25748.057
110.84310.14840.2711.4436-0.49751.2101-0.00830.1681-0.0764-0.119-0.0606-0.0767-0.02920.06520.06230.12490.0040.00230.1171-0.00680.094623.6759-56.103214.5007
120.915-0.12140.17750.7122-0.27332.3459-0.10010.08830.2460.2597-0.08030.2111-0.8789-0.38090.21020.48750.0144-0.10350.17950.01940.305720.0098-29.007718.9086
131.1472-0.19280.46050.6999-0.18211.5191-0.0448-0.06910.10660.1275-0.0345-0.0251-0.32320.02380.05480.2417-0.0197-0.02580.1288-0.01050.135225.8955-44.11828.2875
141.25172.52510.35755.08910.60721.14880.0752-0.034-0.24590.6133-0.1815-1.1928-0.22460.36190.04210.3012-0.0878-0.11420.25170.05990.282641.339-47.73935.2257
150.818-0.0770.4950.5702-0.34860.9887-0.0579-0.08740.11580.142-0.0383-0.1547-0.35080.10280.09410.3196-0.0419-0.06250.17870.00640.166933.4623-43.850734.5635
160.8648-0.04620.32090.7318-0.23841.2019-0.07970.02640.12480.0266-0.0101-0.0089-0.34810.09860.07430.2459-0.0211-0.01690.13630.00710.129724.7569-41.764520.4938
171.86340.8179-0.00714.4540.00391.97710.0270.0208-0.2770.1577-0.0821-0.53650.21910.43610.07950.23060.0034-0.05160.26050.03860.242841.999-56.592826.9891
180.9220.41480.22090.77310.87441.0984-0.00220.21010.0145-0.1427-0.07420.1558-0.27010.13930.04250.2066-0.02360.00210.16350.03310.125926.3843-45.683814.4298
191.2640.55680.10721.1187-0.08311.186-0.0687-0.0198-0.1513-0.02930.0983-0.03780.14370.0807-0.01610.11660.0072-0.00750.09680.0090.120860.4277-23.36958.2171
200.97350.3288-0.37791.8017-0.60041.0819-0.18630.00480.1406-0.1840.33450.89780.1178-0.4208-0.11270.2427-0.1119-0.10040.3620.0980.363535.1275-22.687746.9741
210.90570.2811-0.31831.2946-0.49491.0689-0.060.10780.0869-0.19860.12710.2248-0.021-0.1406-0.06030.1711-0.0228-0.0530.15610.040.1751.1511-12.999946.1532
223.65662.14392.87972.710.46073.2955-0.3840.94980.0731-0.54610.4336-0.0518-0.17030.7574-0.03060.3462-0.1216-0.02870.31850.02740.179361.5231-10.518532.3538
230.71710.4409-0.3280.9686-0.36530.9519-0.07310.21330.0654-0.30270.16590.17580.014-0.0514-0.06770.2475-0.0668-0.06430.19480.06450.19755.2506-9.25337.8542
240.97790.2905-0.1771.0693-0.35670.9492-0.04970.08820.0033-0.24790.13390.18640.1392-0.1782-0.07750.1896-0.0344-0.04640.15010.02750.189448.5458-20.416848.5785
253.45780.43511.68972.36370.28213.8958-0.15520.3324-0.0499-0.33630.093-0.4083-0.02550.50190.07590.249-0.04960.03810.26510.02090.225370.0119-16.802439.319
260.5459-0.64640.38410.8126-0.59461.664-0.0731-0.1702-0.1463-0.18040.0930.110.2364-0.1108-0.04180.2011-0.0402-0.01710.1291-0.00240.182652.7519-25.94751.1178
271.3358-0.2118-0.06461.44960.23170.6223-0.0293-0.1414-0.07520.08790.0338-0.08660.1485-0.04310.00810.1326-0.00240.00590.11680.01250.124452.8365-61.416360.3056
280.69760.15160.07612.7638-0.17071.15940.02140.36480.0142-0.66080.0801-0.63550.2840.01550.02490.25840.01090.14580.2664-0.04710.459874.4176-62.811243.1047
291.3330.2008-0.28551.60580.20871.5464-0.08370.26610.1872-0.25120.0737-0.2684-0.1235-0.08220.03760.1729-0.02020.02820.15010.02430.262162.2628-40.953754.1021
300.6774-0.01180.21322.12140.02351.3339-0.00240.13230.1253-0.4351-0.0514-0.3355-0.09880.14040.02280.2265-0.00720.07370.15530.03130.259164.4356-47.457645.784
310.10530.52650.11812.79620.7210.30750.0532-0.1059-0.09250.2960.0178-0.56030.10040.0628-0.02240.1830.0218-0.05280.16630.00050.300769.6307-60.04464.7884
321.11290.2213-0.09222.12330.20580.919-0.0280.0960.0732-0.19310.0141-0.2470.00780.037-0.00320.1548-0.00440.06130.12690.01550.199862.9141-51.731849.138
337.9893-0.4712-1.16031.7746-0.54360.37980.1793-0.86690.93880.17410.0591-0.5122-0.17250.2977-0.09010.1867-0.0146-0.02770.209-0.07750.441468.9054-38.180163.8793
340.65190.03460.02351.18620.32930.582-0.0066-0.01790.1161-0.08760.0047-0.3772-0.08310.10430.01250.171-0.01020.04540.13760.00370.351968.3343-41.708255.8324
350.8085-0.13410.04481.3010.14420.8799-0.01650.0394-0.0174-0.0774-0.0014-0.3730.01360.11320.01460.15320.01220.03530.13590.01680.237565.6061-57.941752.3047
364.01-0.3021-0.69471.8305-0.1951.8270.0108-0.4280.5230.47480.0496-0.0796-0.1774-0.0406-0.02610.24470.0004-0.0140.1976-0.06130.278361.5291-44.187671.3136
371.27220.9607-0.06890.9708-0.44860.649-0.03440.0725-0.18980.0587-0.0593-0.27330.21-0.07650.09720.1560.0316-0.00580.12950.01720.222463.2122-62.439657.6253
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 34 )
2X-RAY DIFFRACTION2chain 'A' and (resid 35 through 50 )
3X-RAY DIFFRACTION3chain 'A' and (resid 51 through 70 )
4X-RAY DIFFRACTION4chain 'A' and (resid 71 through 115 )
5X-RAY DIFFRACTION5chain 'A' and (resid 116 through 153 )
6X-RAY DIFFRACTION6chain 'A' and (resid 154 through 165 )
7X-RAY DIFFRACTION7chain 'A' and (resid 166 through 189 )
8X-RAY DIFFRACTION8chain 'A' and (resid 190 through 218 )
9X-RAY DIFFRACTION9chain 'A' and (resid 219 through 237 )
10X-RAY DIFFRACTION10chain 'A' and (resid 238 through 260 )
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 34 )
12X-RAY DIFFRACTION12chain 'B' and (resid 35 through 50 )
13X-RAY DIFFRACTION13chain 'B' and (resid 51 through 153 )
14X-RAY DIFFRACTION14chain 'B' and (resid 154 through 166 )
15X-RAY DIFFRACTION15chain 'B' and (resid 167 through 189 )
16X-RAY DIFFRACTION16chain 'B' and (resid 190 through 218 )
17X-RAY DIFFRACTION17chain 'B' and (resid 219 through 237 )
18X-RAY DIFFRACTION18chain 'B' and (resid 238 through 260 )
19X-RAY DIFFRACTION19chain 'C' and (resid 2 through 34 )
20X-RAY DIFFRACTION20chain 'C' and (resid 35 through 50 )
21X-RAY DIFFRACTION21chain 'C' and (resid 51 through 153 )
22X-RAY DIFFRACTION22chain 'C' and (resid 154 through 165 )
23X-RAY DIFFRACTION23chain 'C' and (resid 166 through 189 )
24X-RAY DIFFRACTION24chain 'C' and (resid 190 through 218 )
25X-RAY DIFFRACTION25chain 'C' and (resid 219 through 237 )
26X-RAY DIFFRACTION26chain 'C' and (resid 238 through 260 )
27X-RAY DIFFRACTION27chain 'D' and (resid 2 through 34 )
28X-RAY DIFFRACTION28chain 'D' and (resid 35 through 50 )
29X-RAY DIFFRACTION29chain 'D' and (resid 51 through 70 )
30X-RAY DIFFRACTION30chain 'D' and (resid 71 through 97 )
31X-RAY DIFFRACTION31chain 'D' and (resid 98 through 115 )
32X-RAY DIFFRACTION32chain 'D' and (resid 116 through 153 )
33X-RAY DIFFRACTION33chain 'D' and (resid 154 through 166 )
34X-RAY DIFFRACTION34chain 'D' and (resid 167 through 189 )
35X-RAY DIFFRACTION35chain 'D' and (resid 190 through 218 )
36X-RAY DIFFRACTION36chain 'D' and (resid 219 through 237 )
37X-RAY DIFFRACTION37chain 'D' and (resid 238 through 260 )

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