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- PDB-7yxv: Crystal structure of a tautomerase superfamily member form Acinet... -

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Entry
Database: PDB / ID: 7yxv
TitleCrystal structure of a tautomerase superfamily member form Acinetobacter baumanii
ComponentsAnthranilate synthase
KeywordsCYTOSOLIC PROTEIN / tautomerase superfamily / 4-oxalocrotonate tautomerase / T6SS
Function / homologyTautomerase, MSAD family / Tautomerase enzyme / Tautomerase/MIF superfamily / NITRATE ION / Anthranilate synthase
Function and homology information
Biological speciesAcinetobacter baumannii (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsPankov, G. / Hunter, W.N.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust215599/Z/19/Z United Kingdom
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: The structure of a tautomerase superfamily member linked to the type VI secretion system of Acinetobacter baumannii.
Authors: Pankov, G. / Mol Avelar, G. / Buchanan, G. / Coulthurst, S.J. / Hunter, W.N.
History
DepositionFeb 16, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: 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: Anthranilate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4133
Polymers15,3161
Non-polymers972
Water2,396133
1
A: Anthranilate synthase
hetero molecules

A: Anthranilate synthase
hetero molecules

A: Anthranilate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2399
Polymers45,9473
Non-polymers2926
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area7810 Å2
ΔGint-47 kcal/mol
Surface area15240 Å2
Unit cell
Length a, b, c (Å)59.185, 59.185, 97.757
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-368-

HOH

21A-427-

HOH

31A-431-

HOH

41A-432-

HOH

51A-433-

HOH

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Components

#1: Protein Anthranilate synthase / Anthranilate synthase component II / Tautomerase / Tautomerase enzyme family protein / Tautomerase ...Anthranilate synthase component II / Tautomerase / Tautomerase enzyme family protein / Tautomerase family protein


Mass: 15315.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter baumannii (bacteria)
Gene: A7M90_11190, AB945B12_02656, Aba9201_05520, ABR2091_1504, ABUW_2349, ACX61_10775, APC21_13445, C6N18_08520, CBE85_12580, E1A86_09085, E1A87_16805, EA686_20000, EA706_14840, EGM95_12490, F2P40_ ...Gene: A7M90_11190, AB945B12_02656, Aba9201_05520, ABR2091_1504, ABUW_2349, ACX61_10775, APC21_13445, C6N18_08520, CBE85_12580, E1A86_09085, E1A87_16805, EA686_20000, EA706_14840, EGM95_12490, F2P40_09685, FGL68_10230, FJU36_18545, FR761_08425, G3N53_00085, GNY86_01620, GSE42_08590, GUK62_04465, H0529_06935, HB367_04115, NCTC13421_02212, SAMEA104305385_02323, SI89_13245
Production host: Escherichia coli (E. coli) / References: UniProt: A0A077GKT8
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.15 Å3/Da / Density % sol: 42.87 % / Description: Rhomboid prisms
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 1 ul protein (20 mM HEPES-NaOH pH 6.8, 150 mM NaCl) mixed with 1 ul of reservoir solution (0.2 M NH4NO3 and 20% w/v PEG3350)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Aug 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→45.394 Å / Num. obs: 13698 / % possible obs: 97.3 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.023 / Rrim(I) all: 0.051 / Net I/σ(I): 4.1
Reflection shellResolution: 1.7→1.73 Å / Num. unique obs: 658 / CC1/2: 0.951 / % possible all: 87

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LKB

4lkb


Resolution: 1.7→45.39 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.936 / SU B: 1.721 / SU ML: 0.057 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1863 675 4.9 %RANDOM
Rwork0.137 ---
obs0.1394 13022 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.59 Å2 / Biso mean: 13.072 Å2 / Biso min: 4.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 1.7→45.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1011 0 5 133 1149
Biso mean--13.54 24.84 -
Num. residues----121
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0191090
X-RAY DIFFRACTIONr_bond_other_d0.0020.021060
X-RAY DIFFRACTIONr_angle_refined_deg1.9691.9671473
X-RAY DIFFRACTIONr_angle_other_deg1.03932474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6265128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69323.8657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38615224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.821510
X-RAY DIFFRACTIONr_chiral_restr0.1210.2164
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211166
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02220
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 59 -
Rwork0.161 881 -
all-940 -
obs--88.01 %

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