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- PDB-3pf6: The structure of uncharacterized protein PP-LUZ7_gp033 from Pseud... -

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Basic information

Entry
Database: PDB / ID: 3pf6
TitleThe structure of uncharacterized protein PP-LUZ7_gp033 from Pseudomonas phage LUZ7.
Componentshypothetical protein PP-LUZ7_gp033
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / dsDNA viruses
Function / homologySingle alpha-helices involved in coiled-coils or other helix-helix interfaces - #2290 / : / Domain of unknown function (DUF6833) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / DUF6833 domain-containing protein
Function and homology information
Biological speciesPseudomonas phage LUZ7 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsCuff, M.E. / Evdokimova, E. / Liu, F. / Edwards, A. / Savchenko, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of uncharacterized protein PP-LUZ7_gp033 from Pseudomonas phage LUZ7.
Authors: Cuff, M.E. / Evdokimova, E. / Liu, F. / Edwards, A. / Savchenko, A. / Joachimiak, A.
History
DepositionOct 28, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 10, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 20, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein PP-LUZ7_gp033
B: hypothetical protein PP-LUZ7_gp033
C: hypothetical protein PP-LUZ7_gp033
D: hypothetical protein PP-LUZ7_gp033
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8039
Polymers28,6264
Non-polymers1775
Water6,503361
1
A: hypothetical protein PP-LUZ7_gp033
D: hypothetical protein PP-LUZ7_gp033
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3844
Polymers14,3132
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-67 kcal/mol
Surface area6370 Å2
MethodPISA
2
B: hypothetical protein PP-LUZ7_gp033
C: hypothetical protein PP-LUZ7_gp033
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4195
Polymers14,3132
Non-polymers1063
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-80 kcal/mol
Surface area6250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.886, 40.822, 46.268
Angle α, β, γ (deg.)70.140, 84.610, 83.860
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
hypothetical protein PP-LUZ7_gp033


Mass: 7156.506 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage LUZ7 (virus) / Gene: PP-LUZ7_gp033 / Plasmid: p11 / Production host: Escherichia coli (E. coli) / Strain (production host): modified BL21(DE3) / References: UniProt: C8ZKC7
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 361 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsAT THIS POSITION, THE ELECTRON DENSITY IN ALL CASES WAS CLEARLY PHE. IT WAS NOT ENGINEERED ON PURPOSE.

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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: 37.36 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 5.7
Details: 0.2M NaCl, 0.1M tri-sodium citrate pH 5.7, 29% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97923 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 14, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionRedundancy: 5.8 % / Av σ(I) over netI: 12.48 / Number: 162142 / Rmerge(I) obs: 0.123 / Χ2: 1.5 / D res high: 1.6 Å / D res low: 50 Å / Num. obs: 27869 / % possible obs: 96.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.345095.510.1242.3585.4
3.454.3498.110.1011.6815.7
3.013.4598.710.1081.8665.9
2.743.0197.810.1161.8585.9
2.542.7498.110.1241.8535.9
2.392.5497.810.1241.6995.9
2.272.3997.910.1191.6335.9
2.172.2797.310.1321.7555.9
2.092.1797.310.1331.5775.9
2.022.0996.810.1471.625.9
1.952.0296.710.141.3635.9
1.91.9596.610.1681.6975.9
1.851.996.610.1541.2215.9
1.81.8595.910.1611.1195.9
1.761.895.910.1761.0875.9
1.721.7695.710.1871.0015.9
1.691.7295.410.1971.1456
1.661.6995.910.2151.1115.9
1.631.6694.810.2311.0855.7
1.61.6395.210.2451.1415.1
ReflectionResolution: 1.6→50 Å / Num. all: 27869 / Num. obs: 27869 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 13.8 Å2 / Rmerge(I) obs: 0.123 / Χ2: 1.495 / Net I/σ(I): 15.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.6-1.635.10.24513591.14195.2
1.63-1.665.70.23113561.08594.8
1.66-1.695.90.21514151.11195.9
1.69-1.7260.19713491.14595.4
1.72-1.765.90.18713941.00195.7
1.76-1.85.90.17613871.08795.9
1.8-1.855.90.16113861.11995.9
1.85-1.95.90.15413811.22196.6
1.9-1.955.90.16813801.69796.6
1.95-2.025.90.1414021.36396.7
2.02-2.095.90.14713831.6296.8
2.09-2.175.90.13314211.57797.3
2.17-2.275.90.13214181.75597.3
2.27-2.395.90.11913921.63397.9
2.39-2.545.90.12414011.69997.8
2.54-2.745.90.12414271.85398.1
2.74-3.015.90.11613941.85897.8
3.01-3.455.90.10814221.86698.7
3.45-4.345.70.10114141.68198.1
4.34-505.40.12413882.35895.5

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.6 Å / D res low: 43.43 Å / FOM : 0 / FOM acentric: 0.336 / FOM centric: 0 / Reflection: 0 / Reflection acentric: 27700 / Reflection centric: 0
Phasing MAD setR cullis acentric: 1.05 / R cullis centric: 0 / Highest resolution: 1.6 Å / Lowest resolution: 43.43 Å / Loc acentric: 0.1 / Loc centric: 0 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 27700 / Reflection centric: 0
Phasing MAD set shell

ID: 1 / R cullis centric: 0 / Loc centric: 0 / Power acentric: 0 / Power centric: 0 / Reflection centric: _

Resolution (Å)R cullis acentricLoc acentricReflection acentric
10.18-43.431.120.374
5.76-10.181.010.3490
4.02-5.760.990.41184
3.09-4.020.910.32143
2.5-3.0910.23445
2.11-2.51.030.24948
1.82-2.111.140.16754
1.6-1.821.30.18662
Phasing MAD set site

Atom type symbol: Se / Occupancy iso: 0

IDB isoFract xFract yFract zOccupancy
115.23380.9230.550.6713.147
215.51550.9730.2010.7932.779
316.35740.8870.7970.3582.749
416.09241.446-0.0241.0543.122
519.57830.8690.5870.5632.961
617.25840.4160.5270.5862.969
718.07880.9380.8760.0522.624
821.4150.4170.4680.5023.508
918.58331.4430.0881.0852.835
1022.01950.990.9980.0012.339
1125.38960.70.6710.061.848
1224.87471.1690.5750.8391.276
1328.93751.2630.5570.8261.875
1420.23280.550.6220.0931.062
1526.30140.6010.690.0731.245
1626.4111.140.6020.8911.074
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflection acentricReflection centric
10.18-43.4300.3250740
5.76-10.1800.37104900
4.02-5.7600.353011840
3.09-4.0200.348021430
2.5-3.0900.386034450
2.11-2.500.383049480
1.82-2.1100.337067540
1.6-1.8200.282086620
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 27700
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
5.96-10064.50.84501
4.8-5.9658.20.925509
4.2-4.854.90.928503
3.78-4.259.60.932589
3.47-3.7863.50.918636
3.22-3.4759.60.931699
3.02-3.2258.20.909739
2.85-3.0257.50.909786
2.71-2.8554.90.903813
2.58-2.71590.903883
2.48-2.5858.20.91905
2.38-2.48560.91955
2.3-2.38570.911966
2.22-2.360.20.9081037
2.15-2.2254.10.9091032
2.09-2.1554.10.9031086
2.03-2.0960.30.8881095
1.98-2.0360.60.8841140
1.93-1.9860.80.8741163
1.88-1.9362.10.8831185
1.84-1.8862.70.8771221
1.8-1.8461.70.8821225
1.76-1.861.90.8611259
1.73-1.76660.8541312
1.69-1.7364.90.8571286
1.66-1.6963.80.8461342
1.63-1.6667.10.7971351
1.6-1.6369.90.7651482

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6.1phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→31.64 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.1915 / WRfactor Rwork: 0.1551 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.9364 / SU B: 2.67 / SU ML: 0.044 / SU R Cruickshank DPI: 0.0799 / SU Rfree: 0.0793 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.079
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1647 1409 5.1 %RANDOM
Rwork0.1346 ---
all0.1361 27737 --
obs0.1361 27737 96.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 51.16 Å2 / Biso mean: 17.5547 Å2 / Biso min: 5.85 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å2-0.05 Å20.5 Å2
2---0.57 Å21.39 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.6→31.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 5 361 2188
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211941
X-RAY DIFFRACTIONr_bond_other_d0.0010.021308
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.9542637
X-RAY DIFFRACTIONr_angle_other_deg0.87633188
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0615242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.42423.18791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57615324
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.9041513
X-RAY DIFFRACTIONr_chiral_restr0.0810.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02401
X-RAY DIFFRACTIONr_mcbond_it0.8271.51196
X-RAY DIFFRACTIONr_mcbond_other0.2431.5469
X-RAY DIFFRACTIONr_mcangle_it1.49621933
X-RAY DIFFRACTIONr_scbond_it2.3643745
X-RAY DIFFRACTIONr_scangle_it3.8614.5704
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.162 90 -
Rwork0.146 1849 -
all-1939 -
obs--93.18 %
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)
11.0171-0.0123-0.00421.1618-0.57541.413-0.0128-0.0338-0.02620.0081-0.0299-0.04490.00140.01280.04270.01230.0039-0.00050.0129-0.01040.01819.053731.058926.1147
21.02090.0154-0.09140.7329-0.40741.8596-0.0147-0.0186-0.0234-0.0040.0261-0.01420.0266-0.0973-0.01140.01140.0029-0.00510.0121-0.00870.0174-4.424839.69432.2479
31.91370.5149-0.05251.1971-0.36621.68130.004-0.044-0.02120.03020.00980.0510.0108-0.1071-0.01380.01440.0051-0.00420.0165-0.00810.0138-5.237139.56381.2957
41.97760.47160.36561.1938-0.421.59830.0173-0.0398-0.04760.0131-0.0297-0.09510.03490.08130.01240.01460.00450.00070.0113-0.00560.020210.227431.831625.6473
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999

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