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- PDB-9gva: Crystal structure of the gamma carbonic anhydrase from Porphyromo... -

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Basic information

Entry
Database: PDB / ID: 9gva
TitleCrystal structure of the gamma carbonic anhydrase from Porphyromonas gingivalis
ComponentsHexapeptide transferase family protein
KeywordsLYASE / carbonic anhydrase gamma / Porphyromonas gingivalis / metalloenzyme / bacteria
Function / homology: / : / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / transferase activity / Hexapeptide transferase family protein
Function and homology information
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsAngeli, A. / Ferraroni, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Struct.Biol. / Year: 2024
Title: Kinetic and structural studies of gamma-carbonic anhydrase from the oral pathogen Porphyromonas gingivalis.
Authors: Ferraroni, M. / Angeli, A. / De Luca, V. / Capasso, C. / Supuran, C.T.
History
DepositionSep 23, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Hexapeptide transferase family protein
BBB: Hexapeptide transferase family protein
CCC: Hexapeptide transferase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7486
Polymers62,5523
Non-polymers1963
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-146 kcal/mol
Surface area18930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.752, 120.752, 91.310
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Hexapeptide transferase family protein


Mass: 20850.607 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: PG_1211 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7MV79
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.07 Å3/Da / Density % sol: 59.96 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.0 M ammonium sulfate, 0.1 M HEPES, pH 7.5, 2% v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→45.37 Å / Num. obs: 28525 / % possible obs: 95.9 % / Redundancy: 15.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.049 / Rrim(I) all: 0.139 / Net I/σ(I): 18.5
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 15.7 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 4.4 / Num. unique obs: 3118 / CC1/2: 0.928 / Rpim(I) all: 0.289 / Rrim(I) all: 0.823 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→45.37 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.093 / SU ML: 0.118 / Cross valid method: NONE / ESU R: 0.248 / ESU R Free: 0.188
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1965 1452 5.096 %
Rwork0.1654 27042 -
all0.167 --
obs-28494 95.917 %
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: 38.701 Å2
Baniso -1Baniso -2Baniso -3
1-0.553 Å20.277 Å2-0 Å2
2--0.553 Å20 Å2
3----1.795 Å2
Refinement stepCycle: LAST / Resolution: 2.4→45.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3925 0 3 96 4024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0133994
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173753
X-RAY DIFFRACTIONr_angle_refined_deg1.771.6195415
X-RAY DIFFRACTIONr_angle_other_deg1.3271.5738661
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8555515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7922.85193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.89515658
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2841521
X-RAY DIFFRACTIONr_chiral_restr0.0730.2539
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024527
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02824
X-RAY DIFFRACTIONr_nbd_refined0.1860.2886
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.23659
X-RAY DIFFRACTIONr_nbtor_refined0.160.21979
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21896
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2134
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0580.21
X-RAY DIFFRACTIONr_metal_ion_refined0.0890.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2750.214
X-RAY DIFFRACTIONr_nbd_other0.2320.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2030.27
X-RAY DIFFRACTIONr_mcbond_it3.7373.7322069
X-RAY DIFFRACTIONr_mcbond_other3.7363.732068
X-RAY DIFFRACTIONr_mcangle_it5.4195.5892581
X-RAY DIFFRACTIONr_mcangle_other5.4185.5922582
X-RAY DIFFRACTIONr_scbond_it5.3614.5691925
X-RAY DIFFRACTIONr_scbond_other5.3614.5691925
X-RAY DIFFRACTIONr_scangle_it8.0686.5352834
X-RAY DIFFRACTIONr_scangle_other8.0676.5372835
X-RAY DIFFRACTIONr_lrange_it10.34646.5324456
X-RAY DIFFRACTIONr_lrange_other10.33646.4774439
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.2681160.1992095X-RAY DIFFRACTION99.9096
2.462-2.5290.2231060.1821999X-RAY DIFFRACTION100
2.529-2.6030.2431030.1961964X-RAY DIFFRACTION100
2.603-2.6820.226970.1881481X-RAY DIFFRACTION77.9259
2.682-2.770.199860.1821846X-RAY DIFFRACTION100
2.77-2.8670.2161120.1731777X-RAY DIFFRACTION100
2.867-2.9750.22930.1731719X-RAY DIFFRACTION100
2.975-3.0960.205930.1721661X-RAY DIFFRACTION100
3.096-3.2330.208750.1661610X-RAY DIFFRACTION100
3.233-3.3890.21860.1741507X-RAY DIFFRACTION100
3.389-3.5720.176550.1681192X-RAY DIFFRACTION80.6076
3.572-3.7870.164620.1681146X-RAY DIFFRACTION82.7964
3.787-4.0460.184640.151086X-RAY DIFFRACTION84.6834
4.046-4.3680.164570.1431204X-RAY DIFFRACTION100
4.368-4.780.158660.1291115X-RAY DIFFRACTION100
4.78-5.3370.194360.151031X-RAY DIFFRACTION100
5.337-6.1480.205660.176869X-RAY DIFFRACTION100
6.148-7.4960.221310.176782X-RAY DIFFRACTION100
7.496-10.4590.146280.147600X-RAY DIFFRACTION100
10.459-45.370.214200.19357X-RAY DIFFRACTION100

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