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- PDB-8w7x: SPS_Carbonic Anhydrases -

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Basic information

Entry
Database: PDB / ID: 8w7x
TitleSPS_Carbonic Anhydrases
ComponentsSPS_Carbon Anhydrase
KeywordsLYASE / Carbonic anhydrase
Function / homologyBICARBONATE ION
Function and homology information
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChun, I.S. / Kim, M.S.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: structure of SPS_Carbon Anhydrase
Authors: Chun, I.S. / Kim, M.S.
History
DepositionAug 31, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SPS_Carbon Anhydrase
B: SPS_Carbon Anhydrase
C: SPS_Carbon Anhydrase
D: SPS_Carbon Anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,39722
Polymers104,9994
Non-polymers1,39818
Water4,179232
1
A: SPS_Carbon Anhydrase
B: SPS_Carbon Anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,19911
Polymers52,4992
Non-polymers6999
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3230 Å2
ΔGint-135 kcal/mol
Surface area20250 Å2
MethodPISA
2
C: SPS_Carbon Anhydrase
D: SPS_Carbon Anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,19911
Polymers52,4992
Non-polymers6999
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-132 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.414, 92.414, 148.059
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
SPS_Carbon Anhydrase


Mass: 26249.719 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: polymer info: PubMed 25817590 (DOI: https://doi.org/10.1016/j.bmcl.2015.02.068),PubMed 31250619 (DOI: https://doi.org/10.14348/molcells.2019.0029)
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 250 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.47 Å3/Da / Density % sol: 64.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 4000 Ammonium Sulfate Sodium Acetate pH4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→42 Å / Num. obs: 71625 / % possible obs: 99 % / Redundancy: 4.3 % / CC1/2: 0.939 / Net I/σ(I): 9.06
Reflection shellResolution: 2.2→2.28 Å / Num. unique obs: 7087 / CC1/2: 0.971

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X5S

4x5s


Resolution: 2.2→33.73 Å / SU ML: 0.22 / Cross valid method: NONE / σ(F): 1.98 / Phase error: 21.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1998 2014 2.81 %
Rwork0.1662 --
obs0.1672 71611 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→33.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7400 0 68 232 7700
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087682
X-RAY DIFFRACTIONf_angle_d0.93110420
X-RAY DIFFRACTIONf_dihedral_angle_d16.0142834
X-RAY DIFFRACTIONf_chiral_restr0.0591060
X-RAY DIFFRACTIONf_plane_restr0.0061348
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.30971440.23934930X-RAY DIFFRACTION99
2.26-2.320.21981460.21424982X-RAY DIFFRACTION100
2.32-2.380.2251420.1954967X-RAY DIFFRACTION100
2.38-2.460.23061410.19184997X-RAY DIFFRACTION100
2.46-2.550.26451460.1954949X-RAY DIFFRACTION100
2.55-2.650.23731520.19064983X-RAY DIFFRACTION100
2.65-2.770.22681460.18424970X-RAY DIFFRACTION100
2.77-2.920.24781400.19064972X-RAY DIFFRACTION100
2.92-3.10.2341400.19274986X-RAY DIFFRACTION100
3.1-3.340.21151440.18684970X-RAY DIFFRACTION100
3.34-3.680.17561420.16024971X-RAY DIFFRACTION100
3.68-4.210.1731440.14255007X-RAY DIFFRACTION100
4.21-5.30.16081440.12834961X-RAY DIFFRACTION100
5.3-33.730.19081430.16454952X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -22.1034 Å / Origin y: -11.5445 Å / Origin z: -17.2767 Å
111213212223313233
T0.363 Å2-0.0323 Å2-0.0118 Å2-0.2667 Å20.0246 Å2--0.2634 Å2
L0.2472 °20.1161 °20.0826 °2-0.254 °20.0901 °2--0.281 °2
S0.0042 Å °-0.0273 Å °0.0327 Å °-0.0425 Å °-0.0428 Å °0.0048 Å °-0.0219 Å °0.0186 Å °0.0394 Å °
Refinement TLS groupSelection details: all

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