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- PDB-3k93: Crystal structure of phage related exonuclease (YP_719632.1) from... -

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Basic information

Entry
Database: PDB / ID: 3k93
TitleCrystal structure of phage related exonuclease (YP_719632.1) from HAEMOPHILUS SOMNUS 129PT at 2.15 A resolution
Componentsphage related exonuclease
KeywordsHYDROLASE / phage related exonuclease / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyLambda Exonuclease; Chain A - #10 / Lambda Exonuclease; Chain A / PD-(D/E)XK endonuclease-like domain superfamily / Restriction endonuclease type II-like / Alpha-Beta Complex / Alpha Beta / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Function and homology information
Biological speciesHaemophilus somnus 129PT (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.15 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of phage related exonuclease (YP_719632.1) from HAEMOPHILUS SOMNUS 129PT at 2.15 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 15, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _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: phage related exonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2867
Polymers25,8881
Non-polymers3986
Water2,198122
1
A: phage related exonuclease
hetero molecules

A: phage related exonuclease
hetero molecules

A: phage related exonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,85821
Polymers77,6633
Non-polymers1,19518
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7170 Å2
ΔGint-107 kcal/mol
Surface area32980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.369, 113.369, 42.284
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11A-230-

HOH

DetailsCRYSTAL PACKING AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY ANALYSIS SUPPORT THE ASSIGNMENT OF A TRIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein phage related exonuclease


Mass: 25887.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus somnus 129PT (bacteria) / Strain: 129Pt / Gene: HS_1420 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q0I4G3

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Non-polymers , 5 types, 128 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHIS CONSTRUCT (1-222) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT (1-222) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10.0000% Glycerol, 1.0000M NaCl, 30.0000% PEG-600, 0.1M Cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97947
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 8, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979471
ReflectionResolution: 2.15→28.341 Å / Num. obs: 17252 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 32.941 Å2 / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.15-2.217.50.8362.1964712850.836100
2.21-2.277.50.6821.1903312050.682100
2.27-2.337.50.5751.3906512040.575100
2.33-2.47.50.4951.5865411560.495100
2.4-2.487.50.3991.9861211450.399100
2.48-2.577.50.3332.3815210830.333100
2.57-2.677.50.3132.4781410480.313100
2.67-2.787.60.2443.1767010150.244100
2.78-2.97.50.2043.772689750.204100
2.9-3.047.50.1574.770579410.157100
3.04-3.217.50.1285.666418840.128100
3.21-3.47.50.1076.463038440.107100
3.4-3.637.40.0927.258737940.092100
3.63-3.937.40.0817.755267490.081100
3.93-4.37.40.0719.250396830.071100
4.3-4.817.40.0669.746316300.066100
4.81-5.557.30.079.240005460.07100
5.55-6.87.20.0739.334044760.073100
6.8-9.627.10.0619.826513750.061100
9.62-28.346.40.05511.513652140.05596.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.15→28.341 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 9.253 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.16
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. SODIUM (NA) AND CHLORIDE (CL) IONS, GLYCEROL (GOL), AND POLYETHYLENE GLYCOL (PEG) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 5. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 874 5.1 %RANDOM
Rwork0.172 ---
obs0.174 17249 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.03 Å2 / Biso mean: 18.489 Å2 / Biso min: 3.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0.07 Å20 Å2
2---0.13 Å20 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 2.15→28.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1775 0 23 122 1920
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221858
X-RAY DIFFRACTIONr_bond_other_d0.0020.021279
X-RAY DIFFRACTIONr_angle_refined_deg1.4591.9622508
X-RAY DIFFRACTIONr_angle_other_deg0.97133132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3735232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.59725.22290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.76515338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0131510
X-RAY DIFFRACTIONr_chiral_restr0.1020.2275
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022058
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02364
X-RAY DIFFRACTIONr_mcbond_it0.7531.51124
X-RAY DIFFRACTIONr_mcbond_other0.1671.5456
X-RAY DIFFRACTIONr_mcangle_it1.44521821
X-RAY DIFFRACTIONr_scbond_it2.2713734
X-RAY DIFFRACTIONr_scangle_it3.7654.5682
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 63 -
Rwork0.255 1213 -
all-1276 -
obs--100 %
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)
11.83141.6467-0.06083.02340.7652.0676-0.09180.0755-0.0487-0.10490.02-0.0591-0.0081-0.01020.07180.06590.04010.03830.10470.01020.22216.49350.1324.885
22.6639-0.9338-1.85231.29360.24892.0191-0.0792-0.1395-0.3007-0.0201-0.0553-0.11830.20650.07170.13460.0753-0.02840.02190.09110.0030.3179-2.23639.62913.444
33.10.2285-0.73570.72960.18340.8363-0.04120.1124-0.4235-0.0303-0.0753-0.00530.1097-0.0780.11640.08270.02290.00350.04780.02630.17920.02543.61410.67
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 53
2X-RAY DIFFRACTION2A54 - 139
3X-RAY DIFFRACTION3A140 - 222

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