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- PDB-3sm4: Crystal Structure of the K131A Mutant of Lambda Exonuclease in Co... -

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Basic information

Entry
Database: PDB / ID: 3sm4
TitleCrystal Structure of the K131A Mutant of Lambda Exonuclease in Complex with a 5'-Phosphorylated 14-mer/12-mer Duplex and Magnesium
Components
  • 5'-D(*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3'
  • 5'-D(P*AP*GP*CP*TP*AP*CP*TP*GP*TP*AP*CP*CP*GP*A)-3'
  • Exonuclease
KeywordsHYDROLASE/DNA / homologous recombination / DNA repair / recombineering / single-strand annealing / Type II Restriction Endonuclease Fold / 5'-3' dsDNA exonuclease / HYDROLASE-DNA complex
Function / homology
Function and homology information


exodeoxyribonuclease (lambda-induced) / exonuclease activity / metal ion binding
Similarity search - Function
YqaJ viral recombinase / YqaJ-like viral recombinase domain / Lambda 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
Similarity search - Domain/homology
PHOSPHATE ION / DNA / DNA (> 10) / Exonuclease
Similarity search - Component
Biological speciesEnterobacteria phage lambda (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsBell, C.E. / Zhang, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structures of {lambda} exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity.
Authors: Zhang, J. / McCabe, K.A. / Bell, C.E.
History
DepositionJun 27, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 20, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2011Group: Database references / Experimental preparation / Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_sheet.number_strands / _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: Exonuclease
B: Exonuclease
C: Exonuclease
D: 5'-D(*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3'
E: 5'-D(P*AP*GP*CP*TP*AP*CP*TP*GP*TP*AP*CP*CP*GP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,77111
Polymers86,4615
Non-polymers3096
Water10,521584
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-127 kcal/mol
Surface area35160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.391, 78.391, 247.534
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Exonuclease /


Mass: 26164.758 Da / Num. of mol.: 3 / Mutation: K131A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage lambda (virus) / Gene: exo, Lambda Exonuclease, red-alpha, redX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-AI
References: UniProt: P03697, exodeoxyribonuclease (lambda-induced)

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DNA chain , 2 types, 2 molecules DE

#2: DNA chain 5'-D(*TP*CP*GP*GP*TP*AP*CP*AP*GP*TP*AP*G)-3'


Mass: 3702.428 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: DNA chain 5'-D(P*AP*GP*CP*TP*AP*CP*TP*GP*TP*AP*CP*CP*GP*A)-3'


Mass: 4264.793 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: 5'-phosphorylated

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Non-polymers , 4 types, 590 molecules

#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 584 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 19% PEG3350, 0.2 M sodium bromide, 5 mM magnesium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Aug 3, 2010
RadiationMonochromator: Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.563
11-H-K, K, -L20.437
ReflectionResolution: 1.88→67.9 Å / Num. all: 65978 / Num. obs: 65978 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 20.3
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 4.2 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AVQ

1avq


Resolution: 1.88→67.89 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.946 / SU B: 5.388 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.026 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.18578 3584 5.2 %RANDOM
Rwork0.15976 ---
all0.16113 65978 --
obs0.16113 65978 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.638 Å2
Baniso -1Baniso -2Baniso -3
1--7.59 Å20 Å20 Å2
2---7.59 Å20 Å2
3---15.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.024 Å0.026 Å
Luzzati sigma a-0.072 Å
Refinement stepCycle: LAST / Resolution: 1.88→67.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5476 533 14 584 6607
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0226218
X-RAY DIFFRACTIONr_angle_refined_deg0.9192.0548517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5365679
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.86323.491275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.92915958
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4651542
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214593
LS refinement shellResolution: 1.879→1.928 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 243 -
Rwork0.249 4805 -
obs--98.65 %
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)
12.37131.31791.33194.47580.737910.55550.23060.13310.0393-0.67160.0404-0.11210.38460.5155-0.2710.27370.0658-0.01960.1326-0.01090.3895-23.829-36.264-10.673
22.074-0.00980.88752.01520.03721.61530.00730.0301-0.06140.00620.0362-0.0609-0.06580.1801-0.04350.06370.02620.01940.0410.01430.1406-19.563-20.7264.285
32.6025-1.7130.90858.1018-3.43662.62110.03390.1165-0.0931-0.05190.07270.555-0.0551-0.2318-0.10660.04640.0146-0.01670.0734-0.01050.126-0.5-31.522-10.767
43.9904-1.383-0.9061.16590.19160.49870.07220.1137-0.4503-0.1025-0.1390.18350.1547-0.0480.06690.1020.0164-0.03090.05280.00540.2019-14.934-37.785-1.191
52.091.5804-0.01674.3935-0.2272-0.07930.0505-0.1305-0.01240.0871-0.04530.12480.0747-0.0005-0.00530.11380.03170.01140.05430.01350.12142.048-30.0940.919
65.1444-0.6185-0.85032.55590.14593.6068-0.0346-0.11220.0079-0.00540.00470.0763-0.0366-0.01210.02990.0530.01520.00160.02640.0480.1083-9.183-34.7537.164
72.5104-0.4923-0.47170.7099-0.19040.4222-0.0593-0.1716-0.18630.07150.07040.12750.0022-0.0271-0.01110.08050.0077-0.01790.02420.0030.1055-13.991-29.3394.649
84.14183.08761.05013.31461.48790.87940.06120.0377-0.20410.14510.0269-0.42440.2470.1927-0.08810.11870.0528-0.0050.11510.00780.209432.691-12.692-9.713
93.09761.2989-0.1454.0057-1.62868.53-0.04540.47990.2562-0.59010.04360.0234-0.3310.10410.00180.1480.0384-0.01270.10980.02180.164220.908-9.279-11.912
102.38881.1482-2.94022.1999-4.368712.85360.0943-0.06970.19920.37820.13870.2069-0.004-0.5431-0.2330.2177-0.00440.01490.1122-0.02890.152111.254-8.8429.927
112.8303-0.6499-1.0733.23613.47614.92830.0256-0.0879-0.04050.1076-0.0062-0.03290.1066-0.0658-0.01940.0160.0068-0.01280.01140.02260.081611.723-17.2421.374
122.43373.9057-0.2976.5378-0.53391.1885-0.14070.2574-0.0133-0.52530.1609-0.09610.177-0.0441-0.02020.14180.0721-0.00940.10210.03130.13976.8351.597-13.605
131.4473-0.92570.32551.5582-0.10280.3531-0.0633-0.05060.2104-0.02530.053-0.1796-0.04730.06550.01030.0446-0.0082-0.01330.0310.00240.142116.1015.512-4.255
140.8704-0.43450.19181.6523-0.1860.3689-0.0576-0.09570.07880.15980.0701-0.10810.0080.0222-0.01240.04320.0184-0.02060.0456-0.0050.096717.849-2.5942.018
154.8991-3.386-4.20813.47793.8834.67940.1443-0.08690.2918-0.1326-0.0194-0.0302-0.08090.3106-0.1250.13810.0484-0.02620.1156-0.00250.1875-22.97326.468-10.21
160.8145-0.73071.19791.9251-1.91475.48420.08660.0216-0.0729-0.0745-0.05850.05370.18040.0151-0.02810.02420.03520.0120.05970.00310.1756-15.49911.2350.373
172.488-0.0572-1.24463.309-1.24138.78070.039-0.0564-0.181-0.033-0.05020.09670.2615-0.12480.01120.01360.01340.00120.0130.01560.1693-7.59512.116-2.208
180.44010.92170.13922.04090.20630.502-0.04250.06940.0605-0.10520.04650.05720.0088-0.0213-0.0040.05360.01310.00540.0730.02270.1678-29.5917.036-7.104
193.6803-1.6362-0.08133.2896-1.0992.2012-0.0489-0.04570.01080.2728-0.075-0.2167-0.12750.00980.1240.0406-0.0251-0.01080.0184-0.01140.1293-27.343-6.7771.197
200.99830.6530.35613.4061.57371.27350.0428-0.04710.03540.2467-0.00210.11890.1246-0.031-0.04060.05210.02480.01920.02590.02260.1187-30.0664.0974.135
215.85721.4782-2.4651.9876-0.6351.60840.0701-0.29760.15890.0827-0.0648-0.0846-0.18720.2319-0.00530.0959-0.0076-0.02960.0449-0.00530.1781-10.10222.1592.239
227.10111.6004-2.03072.6277-0.99683.9151-0.02160.0820.2835-0.17530.1410.42770.1002-0.4537-0.11940.137-0.02730.0120.11790.04140.1163-17.094-3.99119.697
233.0457-0.5916-3.76583.69221.19072.89540.00160.22090.05070.10410.0217-0.3650.0281-0.1766-0.02320.180.00610.01810.164-0.0270.1612-4.318-2.44111.464
240.2683-0.33350.06092.0547-0.5989-0.9073-0.0359-0.0691-0.0313-0.06760.09290.18370.0313-0.0851-0.0570.0626-0.00610.00410.12570.00770.16780.045-10.792-0.849
259.19261.1738-1.77610.1350.5531.4718-0.16040.2491-0.42080.0388-0.00140.00550.1563-0.0640.16170.05460.01-0.00170.05820.02480.14916.947-2.685-5.994
263.43920.1197-1.851.5756-6.51379.46980.48960.03120.716-0.29190.06870.55230.5172-0.2819-0.55820.35510.00530.07240.261-0.02310.3843-7.476-7.1172.346
275.4041.50930.66755.87551.53417.9891-0.06990.0162-0.09140.28130.0688-0.34020.18690.25040.00110.1026-0.02690.00060.13960.05160.1411-8.808-3.99320.565
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 22
2X-RAY DIFFRACTION2A23 - 73
3X-RAY DIFFRACTION3A74 - 94
4X-RAY DIFFRACTION4A95 - 119
5X-RAY DIFFRACTION5A120 - 149
6X-RAY DIFFRACTION6A150 - 171
7X-RAY DIFFRACTION7A172 - 226
8X-RAY DIFFRACTION8B-1 - 13
9X-RAY DIFFRACTION9B14 - 32
10X-RAY DIFFRACTION10B33 - 49
11X-RAY DIFFRACTION11B50 - 71
12X-RAY DIFFRACTION12B72 - 90
13X-RAY DIFFRACTION13B91 - 148
14X-RAY DIFFRACTION14B149 - 226
15X-RAY DIFFRACTION15C-2 - 14
16X-RAY DIFFRACTION16C15 - 52
17X-RAY DIFFRACTION17C53 - 72
18X-RAY DIFFRACTION18C73 - 128
19X-RAY DIFFRACTION19C129 - 147
20X-RAY DIFFRACTION20C148 - 197
21X-RAY DIFFRACTION21C198 - 226
22X-RAY DIFFRACTION22D1 - 4
23X-RAY DIFFRACTION23D5 - 8
24X-RAY DIFFRACTION24D9 - 12
25X-RAY DIFFRACTION25E1 - 4
26X-RAY DIFFRACTION26E5 - 8
27X-RAY DIFFRACTION27E9 - 14

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