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- PDB-7kzw: Crystal structure of FTT_1639c from Francisella tularensis str. t... -

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Basic information

Entry
Database: PDB / ID: 7kzw
TitleCrystal structure of FTT_1639c from Francisella tularensis str. tularensis SCHU S4
ComponentsFTT_1639c
KeywordsUNKNOWN FUNCTION / CSGID / Center for Structural Genomics of Infectious Diseases / NIAID / National Institute of Allergy and Infectious Diseases
Function / homologymembrane / Lipoprotein
Function and homology information
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.34 Å
AuthorsStogios, P.J. / Skarina, T. / Osipiuk, J. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
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 FTT_1639c from Francisella tularensis str. tularensis SCHU S4
Authors: Stogios, P.J.
History
DepositionDec 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_contact_author / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_contact_author.country / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FTT_1639c
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8472
Polymers14,8111
Non-polymers351
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.412, 83.412, 36.850
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z

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Components

#1: Protein FTT_1639c


Mass: 14811.315 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: FTT_1639c / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Magic / References: UniProt: Q5NEJ0
#2: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: PEG 3350 25%, Citric acid 0.1M pH 3.5, 0.3M NDSB211, cryoprotectant trehalose, paratone

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.34→30 Å / Num. obs: 32625 / % possible obs: 98.6 % / Redundancy: 8.4 % / Biso Wilson estimate: 14.29 Å2 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.011 / Net I/σ(I): 61.4
Reflection shellResolution: 1.34→1.36 Å / Redundancy: 3 % / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 1.89 / Num. unique obs: 1394 / CC1/2: 0.736 / Rpim(I) all: 0.314 / % possible all: 84.5

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.34→27.61 Å / SU ML: 0.107 / Cross valid method: FREE R-VALUE / σ(F): 0.32 / Phase error: 22.1945
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1888 1540 4.99 %RANDOM
Rwork0.1769 29340 --
obs0.1775 30880 93.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.68 Å2
Refinement stepCycle: LAST / Resolution: 1.34→27.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1000 0 1 248 1249
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01751053
X-RAY DIFFRACTIONf_angle_d1.50041429
X-RAY DIFFRACTIONf_chiral_restr0.1307157
X-RAY DIFFRACTIONf_plane_restr0.0101185
X-RAY DIFFRACTIONf_dihedral_angle_d12.9001402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.34-1.380.2469890.27011423X-RAY DIFFRACTION51.01
1.38-1.430.23911220.27142576X-RAY DIFFRACTION90.08
1.43-1.490.34951420.31072731X-RAY DIFFRACTION95.73
1.49-1.560.32811390.30882616X-RAY DIFFRACTION93.39
1.56-1.640.22591300.23092760X-RAY DIFFRACTION95.98
1.64-1.740.20411490.18242841X-RAY DIFFRACTION99.97
1.74-1.880.18551680.17082825X-RAY DIFFRACTION100
1.88-2.070.1611790.15422844X-RAY DIFFRACTION99.97
2.07-2.370.17231530.15552851X-RAY DIFFRACTION100
2.37-2.980.20451290.17482908X-RAY DIFFRACTION100
2.98-27.610.15321400.15012965X-RAY DIFFRACTION99.97
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)
11.172831662560.0309401678977-0.8572776050261.285344838670.2636594102350.6862310161120.06537069020750.0859184488604-0.161213501781-0.2328499992060.0291355839335-0.1034113031870.3778402780570.205707475567-0.002612307574040.17575981098-0.005092974782770.003154765813620.126494101463-0.008754204846370.13986244524359.222238130610.27821749569.41342934465
21.75737616509-0.5970435250290.7123634331912.694251142080.753531252241.009956746230.04128662909920.63397085778-0.134774696532-0.8005089267450.103204762476-0.2747841152260.4200256764250.3678536956930.1666658050690.303616303514-0.05515755524150.01164623593850.27136406207-0.01117004910020.10890898010463.118873452822.0413703042-5.27047927768
30.422016198290.3890657995650.06372527980710.862356553396-0.3911933885880.7789025318440.0283280932776-0.01324386428010.05130415587190.0337051118506-0.01051478155320.0149494278728-0.001858742245550.106144642353-1.4858948272E-80.108292603513-0.001178417987840.008573646465310.1136658223240.005271886858780.14324055139655.052675217122.77209904769.63846020455
41.140113846130.18380003704-0.1896921117431.354301947480.6140046037970.4109056293540.01938723944080.0127981645883-0.0284087549059-0.04669018505370.02484404412540.02476128867090.05447825082380.060083946471-2.09456743154E-70.140854586943-0.01040620739270.01138713323160.111008451244-0.001001711045940.14160992019452.258856025311.838246380311.3630761213
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 54 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 96 )
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 141 )
4X-RAY DIFFRACTION4chain 'A' and (resid 142 through 181 )

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