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- PDB-4qvr: 2.3 Angstrom Crystal Structure of Hypothetical Protein FTT1539c f... -

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Basic information

Entry
Database: PDB / ID: 4qvr
Title2.3 Angstrom Crystal Structure of Hypothetical Protein FTT1539c from Francisella tularensis.
ComponentsUncharacterized hypothetical protein FTT_1539c
KeywordsUNKNOWN FUNCTION / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / hypothetical protein FTT_1539c
Function / homology: / Domain of unknown function (DUF6844) / DUF6844 domain-containing protein
Function and homology information
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Ren, G. / Huntley, J.F. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.3 Angstrom Crystal Structure of Hypothetical Protein FTT1539c from Francisella tularensis.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Ren, G. / Huntley, J.F. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized hypothetical protein FTT_1539c


Theoretical massNumber of molelcules
Total (without water)55,3741
Polymers55,3741
Non-polymers00
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.006, 47.424, 55.115
Angle α, β, γ (deg.)91.00, 102.19, 99.50
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Uncharacterized hypothetical protein FTT_1539c


Mass: 55373.891 Da / Num. of mol.: 1 / Fragment: hypothetical protein FTT_1539c
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Strain: SCHU S4 / Gene: FTT_1539c / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q5NES5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.64 Å3/Da / Density % sol: 24.82 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 6.9 mg/ml, 0.25 M Sodium chloride, 0.01 M Tris-HCL buffer pH(8.3), 5mM BME; Screen: PACT (D4), 0.1M MMT buffer (pH 7.0), 25%(w/v) PEG 1500., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 30, 2014 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 15653 / Num. obs: 15653 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 33.1
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 3.4 / Num. unique all: 737 / Rsym value: 0.564 / % possible all: 97.7

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→26.64 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.937 / SU B: 13.383 / SU ML: 0.164
Isotropic thermal model: Thermal Factors Individually Isotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.32 / ESU R Free: 0.223 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22445 757 4.9 %RANDOM
Rwork0.17366 ---
all0.17621 14575 --
obs0.17621 14575 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.735 Å2
Baniso -1Baniso -2Baniso -3
1--1.38 Å21.57 Å22.27 Å2
2---0.17 Å22.48 Å2
3---0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.3→26.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2448 0 0 75 2523
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022554
X-RAY DIFFRACTIONr_bond_other_d0.0010.022437
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.983456
X-RAY DIFFRACTIONr_angle_other_deg0.71735626
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3665329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.70526.087115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.27415430
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.212159
X-RAY DIFFRACTIONr_chiral_restr0.0850.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022955
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02548
X-RAY DIFFRACTIONr_mcbond_it2.8233.9431307
X-RAY DIFFRACTIONr_mcbond_other2.8233.9421306
X-RAY DIFFRACTIONr_mcangle_it4.375.8831639
X-RAY DIFFRACTIONr_mcangle_other4.3695.8851640
X-RAY DIFFRACTIONr_scbond_it3.6224.3961247
X-RAY DIFFRACTIONr_scbond_other3.6214.3971248
X-RAY DIFFRACTIONr_scangle_other5.7796.4171818
X-RAY DIFFRACTIONr_long_range_B_refined8.4832.3972965
X-RAY DIFFRACTIONr_long_range_B_other8.46632.2722945
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 55 -
Rwork0.213 1057 -
obs-1057 97.12 %
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)
12.01161.36462.741510.76574.5776.70720.16880.40540.1421-0.18280.0022-0.2553-0.04410.0842-0.17090.07930.00090.0840.30050.01660.26453.719838.12043.7818
23.42830.05270.44251.74490.37022.9657-0.05130.1351-0.05490.0810.0078-0.0240.0249-0.00380.04350.0524-0.02720.00550.14370.00240.1303-1.961234.847211.9244
35.51533.3659-3.32724.087-3.956811.1056-0.4766-0.4033-0.7426-0.7938-0.5387-0.77781.1860.98141.01530.41270.16080.15860.10410.11750.1623-5.247215.601147.3176
42.8897-0.59360.22040.98340.01472.1115-0.0783-0.00420.28360.28560.0745-0.0551-0.12760.17550.00380.1773-0.0662-0.01490.1083-0.01590.20062.375541.095518.9011
51.7466-0.87380.89084.8697-2.53075.8917-0.2461-0.1450.22830.43990.25330.3105-0.8213-0.7336-0.00720.14290.06920.020.1829-0.02440.2063-6.670146.854416.0667
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A41 - 77
2X-RAY DIFFRACTION2A78 - 135
3X-RAY DIFFRACTION3A136 - 210
4X-RAY DIFFRACTION4A211 - 283
5X-RAY DIFFRACTION5A284 - 426

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