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- PDB-6un9: Crystal Structure of the Q7VLF5_HAEDU protein from Haemophilus du... -

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Basic information

Entry
Database: PDB / ID: 6un9
TitleCrystal Structure of the Q7VLF5_HAEDU protein from Haemophilus ducreyi. Northeast Structural Genomics Consortium Target Hdr25
ComponentsUncharacterized protein
KeywordsUNKNOWN FUNCTION / STRUCTURAL GENOMICS / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / Q7VLF5_HAEDU / HDR25 / PSI-Biology
Function / homologyProtein of unknown function DUF1043 / Z-ring associated protein G-like / Domain of unknown function DUF29 / regulation of cell shape / cell division / plasma membrane / Z-ring associated protein G
Function and homology information
Biological speciesHaemophilus ducreyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsVorobiev, S.M. / Seetharaman, J. / Kolev, M. / Xiao, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Q7VLF5_HAEDU protein from Haemophilus ducreyi. Northeast Structural Genomics Consortium Target Hdr25
Authors: Vorobiev, S.M. / Seetharaman, J. / Kolev, M. / Xiao, R. / Everett, J.K. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
History
DepositionOct 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)51,6744
Polymers51,6744
Non-polymers00
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, monodisperse
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10140 Å2
ΔGint-105 kcal/mol
Surface area16520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.609, 70.609, 504.039
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6
Components on special symmetry positions
IDModelComponents
11A-209-

HOH

21A-215-

HOH

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Components

#1: Protein
Uncharacterized protein


Mass: 12918.530 Da / Num. of mol.: 4 / Mutation: I51M, L72M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus ducreyi (bacteria) / Gene: HD_1495 / Plasmid: HdR25.012 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): + MAGIC / References: UniProt: Q7VLF5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 3.7 Å3/Da / Density % sol: 65.46 %
Crystal growTemperature: 291 K / Method: microbatch / Details: 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 12, 2015
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→60 Å / Num. obs: 33685 / % possible obs: 97.6 % / Redundancy: 34.6 % / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.031 / Rrim(I) all: 0.173 / Χ2: 1.186 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.919.90.90915090.930.1860.9310.65880.2
2.9-3.0231.719070.9750.2150.69699.1
3.02-3.1536.10.88419100.9990.1470.8970.73999.8
3.15-3.3238.20.89219270.9940.1440.9040.743100
3.32-3.5339.10.65319670.9920.1040.6610.79100
3.53-3.832.10.37918550.9930.0680.385295.8
3.8-4.1838.50.19219740.9980.0310.1951.13100
4.18-4.7937.80.11199510.0180.1121.061100
4.79-6.0336.60.093206510.0160.0941.2699.9
6.03-6032.40.061228610.010.0622.52199.6

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Processing

Software
NameVersionClassification
PHENIX1.17rc5_3630refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.8→49.44 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 40.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3734 3294 10.07 %
Rwork0.2957 29430 -
obs0.3032 32724 94.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 203.59 Å2 / Biso mean: 95.332 Å2 / Biso min: 36.46 Å2
Refinement stepCycle: final / Resolution: 2.8→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2200 0 0 48 2248
Biso mean---71.6 -
Num. residues----269
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8-2.840.385940.337481891263
2.84-2.880.38171150.3481948106376
2.88-2.930.40391520.3381307145998
2.93-2.980.41011360.32971253138998
2.98-3.030.3691470.30671297144499
3.03-3.080.35391470.31531280142798
3.08-3.140.44461450.29781285143099
3.14-3.20.42821350.30211303143898
3.21-3.270.36791360.3111248138499
3.28-3.350.41351470.300313261473100
3.35-3.430.47211430.322112531396100
3.43-3.530.48641520.420213451497100
3.53-3.630.67371180.52391033115183
3.63-3.750.58221000.5407921102170
3.75-3.880.4551460.334712881434100
3.88-4.040.36421330.30371200133393
4.04-4.220.30431450.240513091454100
4.22-4.440.31181470.242513071454100
4.44-4.720.27371440.211612971441100
4.72-5.090.30471400.21871261140198
5.09-5.60.35291420.26651253139598
5.6-6.410.43481460.326813241470100
6.41-8.060.30861410.28912831424100
8.07-49.440.28671430.2151291143499
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)
10.46830.28870.9740.52860.81962.47360.3759-0.0436-0.12660.0895-0.42010.0580.0358-0.4834-0.00191.56610.1185-0.19980.6659-0.12270.3529-2.20111.1016243.7046
20.6060.18240.76010.42440.25031.42140.3360.1288-0.12970.0846-0.22530.06060.17530.3681-0.0941.4173-0.2921-0.28080.8088-0.02610.24669.211615.0273268.0499
31.13390.45770.97050.42740.20292.09220.24250.2047-0.0229-0.1594-0.2509-0.0163-0.4065-0.1590.0621.5496-0.1796-0.09370.915-0.17190.25372.252422.2425266.5809
40.76450.29931.15240.72760.79971.9930.1642-0.1299-0.0538-0.0073-0.28410.0386-0.25920.4742-0.18251.4850.1055-0.10631.048-0.09080.24793.484517.5229240.3911
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 31 through 99 )A31 - 99
2X-RAY DIFFRACTION2chain 'B' and (resid 34 through 101 )B34 - 101
3X-RAY DIFFRACTION3chain 'C' and (resid 34 through 100 )C34 - 100
4X-RAY DIFFRACTION4chain 'D' and (resid 32 through 98 )D32 - 98

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