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- PDB-8gpp: Acinetobacter baumannii carbonic anhydrase PaaY -

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Basic information

Entry
Database: PDB / ID: 8gpp
TitleAcinetobacter baumannii carbonic anhydrase PaaY
ComponentsCarbonic anhydrase
KeywordsCARBOHYDRATE / Acinetobacter baumannii / carbonic anhydrase / trimer
Function / homology
Function and homology information


: / Hexapeptide repeat proteins / Hexapeptide repeat / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
BICARBONATE ION / Carbonic anhydrase
Similarity search - Component
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsWen, Y. / Jiao, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82072237; 31870132 China
CitationJournal: Structure / Year: 2023
Title: Mechanistic and structural insights into the bifunctional enzyme PaaY from Acinetobacter baumannii.
Authors: Jiao, M. / He, W. / Ouyang, Z. / Qin, Q. / Guo, Y. / Zhang, J. / Bai, Y. / Guo, X. / Yu, Q. / She, J. / Hwang, P.M. / Zheng, F. / Wen, Y.
History
DepositionAug 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Feb 26, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _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
B: Carbonic anhydrase
C: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,76810
Polymers68,3483
Non-polymers4197
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11440 Å2
ΔGint-168 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.073, 93.123, 56.445
Angle α, β, γ (deg.)90.000, 109.410, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 2 through 123 or (resid 124...
21(chain B and (resid 2 through 92 or (resid 93...
31(chain C and (resid 2 through 92 or (resid 93...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROTHRTHR(chain A and (resid 2 through 123 or (resid 124...AA2 - 1239 - 130
12LYSLYSLYSLYS(chain A and (resid 2 through 123 or (resid 124...AA124131
13PROPROSERSER(chain A and (resid 2 through 123 or (resid 124...AA2 - 1909 - 197
21PROPROGLYGLY(chain B and (resid 2 through 92 or (resid 93...BB2 - 929 - 99
22LYSLYSLYSLYS(chain B and (resid 2 through 92 or (resid 93...BB93100
23PROPROSERSER(chain B and (resid 2 through 92 or (resid 93...BB2 - 1909 - 197
31PROPROGLYGLY(chain C and (resid 2 through 92 or (resid 93...CC2 - 929 - 99
32LYSLYSLYSLYS(chain C and (resid 2 through 92 or (resid 93...CC93100
33HISHISSERSER(chain C and (resid 2 through 92 or (resid 93...CC1 - 1908 - 197

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Components

#1: Protein Carbonic anhydrase / PaaY


Mass: 22782.805 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria) / Gene: paaY, ATCC19606_22550 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6F8THQ5
#2: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 1.59 Å3/Da / Density % sol: 33.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M PCTP buffer (propionic acid, cacodylate, bis-tris propane) pH = 8.0, 25% (w/v) PEG 1500

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.09→48.17 Å / Num. obs: 28739 / % possible obs: 97.5 % / Redundancy: 6.6 % / Biso Wilson estimate: 38.04 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1344 / Net I/σ(I): 10.14
Reflection shellResolution: 2.09→2.17 Å / Rmerge(I) obs: 1.439 / Num. unique obs: 2509 / CC1/2: 0.511

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.19_4092refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GPM

8gpm


Resolution: 2.09→48.17 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.16 / Phase error: 30.46 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.255 1998 6.95 %
Rwork0.1968 51914 -
obs0.2008 28739 96.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.27 Å2 / Biso mean: 49.2061 Å2 / Biso min: 26.25 Å2
Refinement stepCycle: final / Resolution: 2.09→48.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4296 0 19 114 4429
Biso mean--60.54 49.81 -
Num. residues----569
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1140X-RAY DIFFRACTION1.117TORSIONAL
12B1140X-RAY DIFFRACTION1.117TORSIONAL
13C1140X-RAY DIFFRACTION1.117TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.09-2.120.4176960.38521335143171
2.12-2.140.38021180.36941609172784
2.15-2.170.31231280.32361705183389
2.17-2.20.34831400.3271852199296
2.2-2.230.39661430.30751908205199
2.23-2.270.34561430.30241906204999
2.27-2.30.29761430.29231909205299
2.3-2.340.3391380.26491902204099
2.34-2.380.3551410.26561910205199
2.38-2.420.34371410.26111896203798
2.42-2.470.30781460.25161882202898
2.47-2.520.30081420.24711858200098
2.52-2.580.33921400.24071877201796
2.58-2.640.26341400.21821850199099
2.64-2.70.26521430.22631922206599
2.7-2.780.29451430.20221908205199
2.78-2.860.22121440.20891913205799
2.86-2.950.22861450.20011908205399
2.95-3.050.3071380.21321846198498
3.05-3.180.28511420.20651862200496
3.18-3.320.25931410.192919462087100
3.32-3.50.27431440.193519002044100
3.5-3.720.261370.17721896203399
3.72-40.2431420.16621913205598
4-4.410.18331380.13981875201398
4.41-5.040.20151400.14171873201398
5.04-6.350.21111400.16571885202597
6.35-48.170.18011430.14541868201198
Refinement TLS params.Method: refined / Origin x: 8.6556 Å / Origin y: 0.7655 Å / Origin z: 14.6631 Å
111213212223313233
T0.2526 Å20.0131 Å20.0006 Å2-0.2589 Å2-0.0069 Å2--0.2231 Å2
L1.2035 °20.0655 °2-0.1279 °2-2.8595 °2-0.5779 °2--1.0433 °2
S-0.0697 Å °-0.0865 Å °-0.0258 Å °0.1176 Å °0.11 Å °-0.0958 Å °-0.0618 Å °-0.0729 Å °-0.0393 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 190
2X-RAY DIFFRACTION1allA201
3X-RAY DIFFRACTION1allB2 - 190
4X-RAY DIFFRACTION1allB201
5X-RAY DIFFRACTION1allC1 - 201
6X-RAY DIFFRACTION1allD1 - 3
7X-RAY DIFFRACTION1allE1
8X-RAY DIFFRACTION1allS1 - 116

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