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- PDB-8uqu: Crystal Structure of N-terminal Domain of Fic Family Protein from... -

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Basic information

Entry
Database: PDB / ID: 8uqu
TitleCrystal Structure of N-terminal Domain of Fic Family Protein from Bordetella bronchiseptica
ComponentsFido domain-containing protein
KeywordsTRANSFERASE / CSBID / Fic / structural genomics / Center for Structural Biology of Infectious Diseases
Function / homologyFido domain-containing protein / Fido-like domain superfamily / Fic/DOC family / Fido domain / Fido domain profile. / ATP binding / D(-)-TARTARIC ACID / Fido domain-containing protein
Function and homology information
Biological speciesBordetella bronchiseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsMinasov, G. / Shuvalova, L. / Brunzelle, J.S. / Kiryukhina, O. / Satchell, K.J.F. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal Structure of N-terminal Domain of Fic Family Protein from Bordetella bronchiseptica
Authors: Minasov, G. / Shuvalova, L. / Brunzelle, J.S. / Kiryukhina, O. / Satchell, K.J.F.
History
DepositionOct 24, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fido domain-containing protein
B: Fido domain-containing protein
C: Fido domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,31722
Polymers124,2363
Non-polymers2,08119
Water2,072115
1
A: Fido domain-containing protein
B: Fido domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,36317
Polymers82,8242
Non-polymers1,53815
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Fido domain-containing protein
hetero molecules

C: Fido domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,90910
Polymers82,8242
Non-polymers1,0858
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Unit cell
Length a, b, c (Å)149.971, 149.971, 371.921
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Fido domain-containing protein


Mass: 41412.137 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BB0907 / Plasmid: pETDuet-1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 / Variant (production host): DE3 Magic / References: UniProt: A0A0H3LJJ5

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Non-polymers , 6 types, 134 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H6O6
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 5.14 Å3/Da / Density % sol: 76.1 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein: 4.5 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 5% Gly, 2mM GDP, 2mM Magnesium chloride; Screen: Classics II (C6), 0.8M Sodium/Potassium tartrate, 0.1M Bis-Tris pH 8.5, 0.5% ...Details: Protein: 4.5 mg/ml, 0.5M Sodium chloride, 0.01M Tris pH 8.3, 5% Gly, 2mM GDP, 2mM Magnesium chloride; Screen: Classics II (C6), 0.8M Sodium/Potassium tartrate, 0.1M Bis-Tris pH 8.5, 0.5% (w/v) PEG 5000 MME; Cryo: 20% Glycerole in screen solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9789 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2021
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 53143 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 16.5 % / Biso Wilson estimate: 78.7 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.05 / Rsym value: 0.199 / Χ2: 1.009 / Net I/σ(I): 16.8
Reflection shellResolution: 2.95→3 Å / Redundancy: 17.2 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2590 / CC1/2: 0.593 / CC star: 0.863 / Rpim(I) all: 0.528 / Χ2: 0.992 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→29.91 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.947 / SU B: 20.12 / SU ML: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.266 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2069 2699 5.1 %RANDOM
Rwork0.1776 ---
obs0.1791 50134 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 180.28 Å2 / Biso mean: 78.553 Å2 / Biso min: 49.47 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20.4 Å20 Å2
2--0.79 Å2-0 Å2
3----2.57 Å2
Refinement stepCycle: final / Resolution: 2.95→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6000 0 137 115 6252
Biso mean--118.48 69.94 -
Num. residues----749
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136258
X-RAY DIFFRACTIONr_bond_other_d0.0010.0155864
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.6438455
X-RAY DIFFRACTIONr_angle_other_deg0.371.5713459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.6175743
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.53620.85353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.409151028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.5821555
X-RAY DIFFRACTIONr_chiral_restr0.0680.2771
X-RAY DIFFRACTIONr_gen_planes_refined0.0540.026999
X-RAY DIFFRACTIONr_gen_planes_other0.0460.021487
LS refinement shellResolution: 2.95→3.026 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 143 -
Rwork0.338 3639 -
all-3782 -
obs--99.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.94441.9018-0.17654.29531.89483.9633-0.11290.1111-0.3041-0.55450.2973-0.1896-0.07040.4798-0.18440.3301-0.0801-0.00630.0813-0.02750.0293-25.212127.69817.9384
211.4437-3.5475-2.99612.37410.85976.83080.0692-0.35450.0644-0.14550.0040.0455-0.5963-0.0478-0.07320.3015-0.0359-0.00870.0448-0.02720.0796-39.760236.607829.6909
33.9232-1.33640.42773.112-0.97882.9859-0.0092-0.0239-0.1243-0.24740.0470.48050.0515-0.7375-0.03790.367-0.0734-0.16560.3211-0.06870.1746-53.23522.497516.2735
41.14180.1725-0.03922.33050.62993.82990.16960.11090.0578-0.3597-0.11470.0618-0.1445-0.1028-0.05490.3659-0.0289-0.09420.0926-0.02930.0938-37.873826.48239.6652
52.77754.44390.232512.71581.75053.78080.2845-0.25430.2265-0.32510.1128-0.0108-0.44540.3185-0.39730.3185-0.08180.05880.1614-0.10910.1611-37.32342.207824.2037
66.1262-0.3051-1.0651.97551.47631.2568-0.160.1189-0.1056-0.40640.06990.1971-0.33830.14420.09020.3663-0.19640.02710.2467-0.11030.0809-16.760236.780314.09
78.48870.56964.19951.73261.01022.4366-0.2257-0.3057-0.03010.25590.13920.10590.0043-0.08480.08650.1432-0.06650.0180.13310.0080.073-19.796235.536541.4796
82.9452-1.09841.13994.0203-0.32432.1931-0.09080.03540.2017-0.27690.0659-0.7130.06610.5380.02490.1492-0.13430.02060.38260.0220.2738-0.577746.517834.7291
92.47280.48770.30423.1922-0.12223.0729-0.00690.3559-0.1243-0.38770.0801-0.35960.27060.4875-0.07320.2513-0.11310.070.2354-0.05830.1112-7.653638.612921.8402
102.17216.0371-1.569120.26962.500414.6209-0.08520.1427-0.1289-0.2781-0.3598-0.1792-0.023-1.5870.4450.0174-0.0050.01150.25050.06270.2068-19.55125.795944.2206
113.6437-0.3356-1.83082.1334-1.05261.63620.0955-0.0353-0.0374-0.4872-0.1261-0.06980.19640.07680.03070.385-0.08980.00940.13130.06440.3262-7.73884.622732.7764
121.308-0.0151-0.19224.0494-0.35612.58770.0278-0.2023-0.00640.2950.1133-0.31840.08570.1658-0.14120.1533-0.1523-0.0760.26160.05050.0648-4.327661.251746.6242
131.581-0.3124-1.48559.7362-5.19224.65230.1566-0.0617-0.42990.1091-0.20550.9440.0231-0.02520.04890.4759-0.35940.07510.5252-0.03240.4916-21.990159.7938.3024
142.67250.28190.05654.1359-0.16431.5376-0.07-0.2810.30880.13020.06270.251-0.2466-0.30010.00730.2574-0.1367-0.03730.26450.01980.1293-11.691776.463539.7965
1512.5295-0.064113.71649.0365-9.535824.93150.45120.1407-0.19260.4541-0.467-0.21550.01740.63990.01580.0743-0.0825-0.0280.15030.00360.091813.959578.534848.1859
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 25
2X-RAY DIFFRACTION2A26 - 49
3X-RAY DIFFRACTION3A50 - 169
4X-RAY DIFFRACTION4A170 - 268
5X-RAY DIFFRACTION5A269 - 282
6X-RAY DIFFRACTION6B1 - 31
7X-RAY DIFFRACTION7B32 - 49
8X-RAY DIFFRACTION8B50 - 172
9X-RAY DIFFRACTION9B173 - 276
10X-RAY DIFFRACTION10B277 - 285
11X-RAY DIFFRACTION11C1 - 35
12X-RAY DIFFRACTION12C36 - 124
13X-RAY DIFFRACTION13C125 - 166
14X-RAY DIFFRACTION14C167 - 275
15X-RAY DIFFRACTION15C276 - 283

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