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- PDB-7rj3: Crystal Structure of the Forkhead Associated (FHA) Domain of the ... -

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Basic information

Entry
Database: PDB / ID: 7rj3
TitleCrystal Structure of the Forkhead Associated (FHA) Domain of the Glycogen Accumulation Regulator (GarA) from Mycobacterium tuberculosis
ComponentsGlycogen accumulation regulator GarA
KeywordsSIGNALING PROTEIN / structural genomics / Center for Structural Genomics of Infectious Diseases / CSGID / FHA / Glycogen Accumulation Regulator
Function / homologyForkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / DI(HYDROXYETHYL)ETHER / Glycogen accumulation regulator GarA
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.68 Å
AuthorsMinasov, G. / Shuvalova, L. / Pshenychnyi, S. / Dubrovska, I. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal Structure of the Forkhead Associated (FHA) Domain of the Glycogen Accumulation Regulator (GarA) from Mycobacterium tuberculosis.
Authors: Minasov, G. / Shuvalova, L. / Pshenychnyi, S. / Dubrovska, I. / Satchell, K.J.F.
History
DepositionJul 20, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycogen accumulation regulator GarA
B: Glycogen accumulation regulator GarA
C: Glycogen accumulation regulator GarA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,1354
Polymers60,0293
Non-polymers1061
Water3,783210
1
A: Glycogen accumulation regulator GarA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,1162
Polymers20,0101
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycogen accumulation regulator GarA


Theoretical massNumber of molelcules
Total (without water)20,0101
Polymers20,0101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Glycogen accumulation regulator GarA


Theoretical massNumber of molelcules
Total (without water)20,0101
Polymers20,0101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.135, 56.755, 92.264
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycogen accumulation regulator GarA


Mass: 20009.754 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: garA, CAB90_02029 / Plasmid: pMCSG53
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A2I7W7N0
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsProtein is hydrolyzed.

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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: 1.96 Å3/Da / Density % sol: 37.2 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 15.3 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris, pH 8.3 against JCSG+ screen G10 (0.15 M potassium bromide, 30% w/v PEG2000 MME)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2019 / Details: Be
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.68→30 Å / Num. obs: 30373 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 20.1 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.027 / Rrim(I) all: 0.07 / Rsym value: 0.065 / Χ2: 1.003 / Net I/σ(I): 26.9
Reflection shellResolution: 1.68→1.71 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.789 / Mean I/σ(I) obs: 2.61 / Num. unique obs: 1511 / CC1/2: 0.806 / CC star: 0.945 / Rpim(I) all: 0.325 / Rrim(I) all: 0.854 / Rsym value: 0.789 / Χ2: 1.003 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6I2P

6i2p


Resolution: 1.68→29.13 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.627 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2228 1531 5 %RANDOM
Rwork0.1744 ---
obs0.1769 28787 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.45 Å2 / Biso mean: 24.285 Å2 / Biso min: 12.31 Å2
Baniso -1Baniso -2Baniso -3
1--1.57 Å20 Å20 Å2
2--1.4 Å20 Å2
3---0.17 Å2
Refinement stepCycle: final / Resolution: 1.68→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 7 219 2599
Biso mean--52.72 32.39 -
Num. residues----311
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0132449
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172289
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.6383325
X-RAY DIFFRACTIONr_angle_other_deg0.3471.5815287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4075314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.47821.301146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.25115385
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4361525
X-RAY DIFFRACTIONr_chiral_restr0.0570.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0540.022828
X-RAY DIFFRACTIONr_gen_planes_other0.0490.02535
LS refinement shellResolution: 1.684→1.728 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 104 -
Rwork0.236 1943 -
all-2047 -
obs--92.25 %
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)
12.78840.46820.77081.98130.35914.861-0.0994-0.015-0.08350.10150.05570.03820.2719-0.1370.04380.0543-0.00670.01420.01680.02050.0459-12.0091.0205-14.4298
24.02250.04020.86532.75150.46632.1954-0.0447-0.17820.19720.18590.03770.0369-0.1215-0.15980.0070.08630.02250.01480.02440.00840.0369-10.299715.1056-16.8735
312.33630.8652.43213.23051.17272.72920.22960.1374-0.1977-0.359-0.1127-0.2810.04560.0176-0.11690.09510.01990.01050.01570.00210.0373-9.62062.7197-30.075
41.8718-0.64660.85993.0717-0.56212.9385-0.0566-0.01390.05750.1285-0.0777-0.2059-0.07220.16440.13420.02980.00270.01070.01620.01880.0378-0.32468.828-19.0331
55.23495.06725.46986.85147.266810.92270.01110.1038-0.1891-0.0215-0.0383-0.02710.1730.06140.02720.05990.01480.02060.020.00120.0582-8.6734-1.8243-19.2872
65.99044.24572.45037.06922.47023.1143-0.0714-0.1899-0.21150.07670.0763-0.17730.02310.0211-0.0050.03330.03450.02230.06740.04070.034-0.4716-17.09435.1541
72.57930.8018-0.0540.54930.01325.80870.0242-0.0629-0.175-0.08180.0604-0.09710.05760.0729-0.08460.048-0.00260.01550.04530.00190.03161.5801-12.6118-5.4048
84.14361.1995-0.15234.65393.85397.27810.0165-0.00710.3312-0.0136-0.0485-0.0288-0.2143-0.14710.0320.04380.02450.00510.01410.00290.0407-3.5778-7.2881-5.1648
94.03790.5429-0.57352.6548-0.81391.198-0.0091-0.10140.2519-0.00360.12750.1353-0.0001-0.1687-0.11840.06050.02560.02170.04330.01690.0311-11.5984-6.6232-1.6807
103.79820.13261.06412.92891.41366.5114-0.0771-0.2557-0.16820.17890.1313-0.21540.1340.1569-0.05420.04730.04380.0070.07330.02680.0357-6.0967-14.23783.6805
117.3864-4.4466-4.60485.37933.549111.39540.09390.26580.8349-0.1373-0.0324-0.0687-0.5673-0.2811-0.06150.03830.0039-0.02310.03740.05290.181414.179611.8183-17.0216
122.21440.2413-1.34970.2001-0.89437.60040.00140.17470.22880.01260.0514-0.0209-0.0311-0.1093-0.05270.01150.00270.0060.0520.02540.065512.14668.8327-19.2236
133.08490.32440.23983.85051.60313.09680.0705-0.1265-0.10140.1296-0.07980.07120.049-0.2610.00930.0408-0.007-0.00890.02720.00510.008214.159-1.3702-13.0692
144.31331.5645-0.14761.6621-0.25573.25240.0699-0.2130.10220.0509-0.1035-0.1505-0.00540.020.03360.0459-0.0135-0.0160.01410.00510.047623.85023.7367-11.7185
152.7305-2.3458-2.47284.38925.03987.19410.08690.0350.3151-0.21210.0221-0.0887-0.21110.0179-0.1090.0329-0.0048-0.01470.00680.02180.088918.385312.5308-14.5241
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A48 - 74
2X-RAY DIFFRACTION2A75 - 103
3X-RAY DIFFRACTION3A104 - 109
4X-RAY DIFFRACTION4A110 - 142
5X-RAY DIFFRACTION5A143 - 152
6X-RAY DIFFRACTION6B47 - 68
7X-RAY DIFFRACTION7B69 - 90
8X-RAY DIFFRACTION8B91 - 107
9X-RAY DIFFRACTION9B108 - 132
10X-RAY DIFFRACTION10B133 - 151
11X-RAY DIFFRACTION11C50 - 64
12X-RAY DIFFRACTION12C65 - 72
13X-RAY DIFFRACTION13C73 - 106
14X-RAY DIFFRACTION14C107 - 142
15X-RAY DIFFRACTION15C143 - 150

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