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- PDB-8dpo: Crystal structure of Neisseria gonorrhoeae carbonic anhydrase wit... -

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Basic information

Entry
Database: PDB / ID: 8dpo
TitleCrystal structure of Neisseria gonorrhoeae carbonic anhydrase with Acetazolamide
ComponentsCarbonic anhydrase
KeywordsLYASE / Carbonic anhydrase / Neisseria gonorrhoeae / Acetazolamide
Function / homology
Function and homology information


carbonic anhydrase / carbonate dehydratase activity / periplasmic space / zinc ion binding
Similarity search - Function
Carbonic anhydrase, prokaryotic-like / 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
5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE / Carbonic anhydrase
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsMarapaka, A.K. / Das, C. / Flaherty, D.P. / Yadav, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R01AI148523 United States
CitationJournal: To Be Published
Title: Crystal structure of Neisseria gonorrhoeae carbonic anhydrase with Acetazolamide
Authors: Marapaka, A.K. / Das, C. / Flaherty, D.P.
History
DepositionJul 15, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_validate_planes
Item: _pdbx_validate_planes.type
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Carbonic anhydrase
C: Carbonic anhydrase
E: Carbonic anhydrase
G: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,47023
Polymers109,2634
Non-polymers2,20719
Water1,820101
1
A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7965
Polymers27,3161
Non-polymers4804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8926
Polymers27,3161
Non-polymers5765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
E: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9887
Polymers27,3161
Non-polymers6726
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
G: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7965
Polymers27,3161
Non-polymers4804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.873, 122.561, 78.214
Angle α, β, γ (deg.)90.000, 117.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Carbonic anhydrase / Carbonate dehydratase


Mass: 27315.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Acetazolamide / Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: cah / Production host: Escherichia coli (E. coli) / References: UniProt: Q50940, carbonic anhydrase
#2: Chemical
ChemComp-AZM / 5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE


Mass: 222.245 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6N4O3S2 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.81 Å3/Da / Density % sol: 56.16 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.2 M NH4H2PO4, 2.2 M (NH4)2SO4 / PH range: 6.4-7.4

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 24, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 36275 / % possible obs: 98 % / Redundancy: 5 % / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.056 / Rrim(I) all: 0.132 / Χ2: 0.478 / Net I/σ(I): 3.8 / Num. measured all: 182689
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.6-2.693.40.34432570.8490.2010.4010.42488.5
2.69-2.84.10.33135680.8820.1790.3790.44497
2.8-2.934.70.31336380.9160.1560.3510.44499.3
2.93-3.085.10.2636680.9470.1230.2890.4699.4
3.08-3.285.40.19436920.9710.0890.2150.47399.6
3.28-3.535.60.13636580.9850.0610.1490.49699.6
3.53-3.885.40.10636930.990.0490.1170.51499.4
3.88-4.455.50.08336770.9920.0380.0920.51299.5
4.45-5.65.50.0737110.9940.0320.0770.4999.2
5.6-105.50.0637130.9960.0270.0660.47998.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.526
Highest resolutionLowest resolution
Rotation46 Å2.74 Å

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Processing

Software
NameVersionClassification
DENZO722data reduction
SCALEPACKdata scaling
MOLREP11.9.02phasing
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KOQ

1koq


Resolution: 2.6→45.99 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.877 / SU B: 11.202 / SU ML: 0.235 / SU R Cruickshank DPI: 0.5691 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.569 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1779 4.9 %RANDOM
Rwork0.192 ---
obs0.1952 34473 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.13 Å2 / Biso mean: 29.382 Å2 / Biso min: 5.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.04 Å20 Å2
3----0 Å2
Refinement stepCycle: final / Resolution: 2.6→45.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6957 0 111 101 7169
Biso mean--41.68 22.12 -
Num. residues----888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0127261
X-RAY DIFFRACTIONr_bond_other_d0.0010.0166362
X-RAY DIFFRACTIONr_angle_refined_deg1.4951.6619907
X-RAY DIFFRACTIONr_angle_other_deg0.4631.55414866
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4235884
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.7921035
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.386101145
X-RAY DIFFRACTIONr_chiral_restr0.0620.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028155
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021381
LS refinement shellResolution: 2.6→2.666 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.344 110 -
Rwork0.272 2102 -
obs--80.97 %

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