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- PDB-8gpm: Acinetobacter baumannii carbonic anhydrase -

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Basic information

Entry
Database: PDB / ID: 8gpm
TitleAcinetobacter baumannii carbonic anhydrase
ComponentsCarbonic anhydrase
KeywordsCARBOHYDRATE / Acinetobacter baumannii / carbonic anhydrase / trimer
Function / homologyHexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / Carbonic anhydrase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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: Acinetobacter baumannii carbonic anhydrase
Authors: Wen, Y. / Jiao, M.
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,0944
Polymers21,8971
Non-polymers1983
Water2,990166
1
A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules

A: Carbonic anhydrase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,28312
Polymers65,6913
Non-polymers5939
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation12_555-y,-z,x1
Buried area11970 Å2
ΔGint-182 kcal/mol
Surface area20760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.698, 108.698, 108.698
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11A-303-

CA

21A-425-

HOH

31A-538-

HOH

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Components

#1: Protein Carbonic anhydrase / PaaY


Mass: 21896.869 Da / Num. of mol.: 1
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / 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.: 166 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-tris pH=6.5, 45% v/v polypropylene glycol P400

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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: Nov 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→34.37 Å / Num. obs: 23637 / % possible obs: 99.92 % / Redundancy: 38.7 % / Biso Wilson estimate: 27.06 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.101 / Net I/σ(I): 28.49
Reflection shellResolution: 1.7→1.76 Å / Num. unique obs: 2337 / CC1/2: 0.832

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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: 1V3W

1v3w


Resolution: 1.7→34.37 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1822 1972 8.34 %
Rwork0.1523 42196 -
obs0.1548 23637 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 109.55 Å2 / Biso mean: 31.3313 Å2 / Biso min: 17.7 Å2
Refinement stepCycle: final / Resolution: 1.7→34.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 16 166 1639
Biso mean--76.92 44.49 -
Num. residues----193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7-1.720.59961500.520816121762
1.72-1.740.44861280.367114921620
1.74-1.760.29421480.278415841732
1.76-1.790.26581440.229815551699
1.79-1.810.20091350.210315901725
1.82-1.840.19951480.203715351683
1.84-1.870.21631380.193815561694
1.87-1.910.23931440.193815941738
1.91-1.940.24551440.19315271671
1.94-1.980.2381420.170415761718
1.98-2.020.19811480.151415391687
2.02-2.060.20621380.132615591697
2.06-2.110.17511500.130715441694
2.11-2.160.1781420.135615591701
2.16-2.220.17021420.147315721714
2.22-2.290.16811450.138615751720
2.29-2.360.1741480.139815751723
2.36-2.440.19561420.131315301672
2.45-2.540.17021380.169416001738
2.54-2.660.22871400.171515691709
2.66-2.80.18221460.159915541700
2.8-2.970.15341390.153315421681
2.97-3.20.15991430.148716011744
3.21-3.520.16431420.144115351677
3.53-4.030.1671380.131215921730
4.04-5.080.14751430.111715521695
5.09-34.370.1791350.161215771712
Refinement TLS params.Method: refined / Origin x: 17.2172 Å / Origin y: -29.817 Å / Origin z: 11.1088 Å
111213212223313233
T0.2116 Å2-0.0122 Å2-0.0059 Å2-0.2062 Å2-0.0178 Å2--0.2013 Å2
L0.856 °2-0.0095 °20.0791 °2-0.628 °2-0.0823 °2--0.5973 °2
S0.0186 Å °0.0843 Å °-0.1036 Å °-0.0938 Å °0.0078 Å °0.0531 Å °0.0616 Å °-0.0509 Å °-0.0197 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 201
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 166

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