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- PDB-4dkw: Structure of P22 Large terminase nuclease domain -

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Basic information

Entry
Database: PDB / ID: 4dkw
TitleStructure of P22 Large terminase nuclease domain
ComponentsLarge terminase protein
KeywordsHYDROLASE / DNA-packaging / Large terminase / Small terminase / nuclease fold / endonuclease / DNA / DNA-packaging motor
Function / homology
Function and homology information


viral terminase complex / viral terminase, large subunit / viral DNA genome packaging / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome organization / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / endonuclease activity / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Nucleotidyltransferase; domain 5 - #280 / Terminase, large subunit BPP22-like / Terminase, large subunit gp17-like, C-terminal / Terminase RNaseH-like domain / Terminase large subunit, T4likevirus-type, N-terminal / Nucleotidyltransferase; domain 5 / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Terminase, large subunit
Similarity search - Component
Biological speciesEnterobacteria phage P22 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsRoy, A. / Cingolani, G.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structure of p22 headful packaging nuclease.
Authors: Roy, A. / Cingolani, G.
History
DepositionFeb 4, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2012Group: Database references
Revision 1.2Aug 29, 2012Group: Database references
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_ncs_dom_lim / 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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Large terminase protein
B: Large terminase protein
C: Large terminase protein
D: Large terminase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,03416
Polymers98,4564
Non-polymers57912
Water20,0331112
1
A: Large terminase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7594
Polymers24,6141
Non-polymers1453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Large terminase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7594
Polymers24,6141
Non-polymers1453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Large terminase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7594
Polymers24,6141
Non-polymers1453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Large terminase protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7594
Polymers24,6141
Non-polymers1453
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.921, 139.795, 61.005
Angle α, β, γ (deg.)90.00, 95.10, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 289 - 482 / Label seq-ID: 1 - 194

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain 'A' and (resseq 289:482 )AA
2chain 'B' and (resseq 289:482 )BB
3chain 'C' and (resseq 289:482 )CC
4chain 'D' and (resseq 289:482 )DD
DetailsThe asymmetric unit contains four identical copies of P22 Large terminase nuclease domain, which is monomeric in solution

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Components

#1: Protein
Large terminase protein / DNA-packaging protein gp2 / Terminase large subunit


Mass: 24613.914 Da / Num. of mol.: 4 / Fragment: nuclease domain (UNP Residues 289-499)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage P22 (virus) / Gene: 2, gene 2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P26745
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1112 / 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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M magnesium sulfate, 20% w/v PEG 3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.972 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Sep 1, 2011
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.493
ReflectionResolution: 2.02→15 Å / Num. obs: 60520 / % possible obs: 90.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 18.4
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3673 / Rsym value: 0.61 / % possible all: 54.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WBN

2wbn


Resolution: 2.02→14.968 Å / σ(F): 1.34 / Phase error: 21.45 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.197 2250 3.72 %thin shells resolution
Rwork0.1656 ---
obs0.1672 60494 81.68 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.4 Å2 / ksol: 0.364 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.9997 Å2-0 Å20.1305 Å2
2---1.9809 Å20 Å2
3---6.9805 Å2
Refinement stepCycle: LAST / Resolution: 2.02→14.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6376 0 28 1112 7516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016588
X-RAY DIFFRACTIONf_angle_d1.0978892
X-RAY DIFFRACTIONf_dihedral_angle_d14.6752388
X-RAY DIFFRACTIONf_chiral_restr0.08860
X-RAY DIFFRACTIONf_plane_restr0.0041168
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1593X-RAY DIFFRACTIONPOSITIONAL0.089
12B1593X-RAY DIFFRACTIONPOSITIONAL0.089
13C1593X-RAY DIFFRACTIONPOSITIONAL0.089
14D1593X-RAY DIFFRACTIONPOSITIONAL0.08
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.06980.37921230.31812594X-RAY DIFFRACTION42
2.0698-2.10650.30361330.30562892X-RAY DIFFRACTION45
2.1065-2.14580.30541220.28923167X-RAY DIFFRACTION52
2.1458-2.18830.30461410.28883622X-RAY DIFFRACTION57
2.1883-2.23440.31451590.27894191X-RAY DIFFRACTION67
2.2344-2.28460.27061720.25084861X-RAY DIFFRACTION77
2.2846-2.33970.29581980.24435434X-RAY DIFFRACTION86
2.3397-2.40050.23991930.22865407X-RAY DIFFRACTION87
2.4005-2.46810.31051900.22755497X-RAY DIFFRACTION88
2.4681-2.54410.22431830.21355604X-RAY DIFFRACTION88
2.5441-2.63040.18411920.19725569X-RAY DIFFRACTION89
2.6304-2.72970.22581950.19155542X-RAY DIFFRACTION89
2.7297-2.8460.22411960.17935579X-RAY DIFFRACTION90
2.846-2.9850.17531460.16725697X-RAY DIFFRACTION91
2.985-3.15590.17631630.15335778X-RAY DIFFRACTION92
3.1559-3.37420.19441550.13595805X-RAY DIFFRACTION92
3.3742-3.66890.18531210.12215792X-RAY DIFFRACTION93
3.6689-4.10410.14582400.10765851X-RAY DIFFRACTION92
4.1041-4.86520.12312030.10145852X-RAY DIFFRACTION94
4.8652-7.01170.16223380.14695753X-RAY DIFFRACTION92
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)
10.9207-0.23330.51750.53770.04982.7927-0.2951-0.05040.26150.3196-0.1693-0.0385-0.37130.07660.05740.52760.0188-0.16620.2289-0.00680.2145-47.035139.6704-39.9787
21.9107-0.6276-0.41281.60080.40920.98620.0409-0.0373-0.26890.05140.06860.37680.3868-0.3322-0.0280.2801-0.1026-0.04030.30250.07460.1551-60.12626.2318-40.845
30.20.05270.02890.4796-0.53871.2468-0.0386-0.06170.08760.20630.11380.214-0.0932-0.069-0.03920.42510.02510.01020.20740.039-0.1212-49.710130.629-34.0819
42.15691.3675-0.96181.56420.00143.079-0.03060.29220.0314-0.3616-0.18260.34750.2127-0.79320.07120.50160.0055-0.11420.3402-0.09190.2339-51.031323.168-53.2382
50.4787-0.0762-0.2971.60860.151.13680.1933-0.16270.0884-0.2232-0.2624-0.163-0.1701-0.0174-0.07070.23510.02880.04950.1740.01110.0882-66.216274.6288-41.5917
60.86760.17070.29660.92530.4311.86290.0174-0.5297-0.33830.5937-0.1321-0.06580.19180.12840.01050.4156-0.0427-0.05820.43870.20950.0782-65.654860.9384-28.7567
71.3567-0.06970.19040.94820.60781.0959-0.04240.0008-0.23770.08270.1383-0.12570.0120.1186-0.09930.199-0.0083-0.02270.14350.00750.1491-59.976665.6124-39.6852
83.4451-0.71251.10412.0798-1.02082.5865-0.1107-0.8159-0.06940.5185-0.11180.4740.1786-0.45010.12540.385-0.07120.16920.2768-0.02450.4034-78.837657.894-36.6829
91.2996-0.54760.24011.01960.10922.16820.09930.241-0.3390.06950.06640.10440.09120.0552-0.10260.30270.0051-0.02960.1328-0.0620.2384-40.964111.704-8.9724
103.172-0.28071.2411.94170.15261.77020.0258-0.05170.34120.1135-0.1478-0.6957-0.51110.4996-0.14850.3816-0.12290.02050.3051-0.04240.1183-27.957225.1365-7.2654
110.8045-0.23040.2380.32050.60671.74970.03320.1211-0.06370.18930.0163-0.12330.0660.225-0.01210.3105-0.0120.01370.1658-0.00790.0723-39.435820.6845-2.5797
121.8570.2178-0.36761.50550.3965.38450.03250.11460.1222-0.25910.05-0.1526-0.5570.72680.06390.33220.01-0.03580.39610.02610.0444-34.622728.3295-21.0934
132.20630.1129-0.11971.07960.26520.8563-0.1663-0.104-0.31860.07390.2687-0.39760.18690.29480.10340.2640.01150.15070.1992-0.05010.2662-35.456646.622-50.6983
141.32680.1345-0.17981.29850.02762.032-0.01980.48560.2064-0.46620.0032-0.2265-0.08260.17620.00110.2386-0.03380.06790.27470.08560.1793-35.284260.1251-63.751
152.2609-0.002-0.33310.55510.08211.1484-0.1535-0.03570.0262-0.02710.2021-0.0930.09530.0176-0.01140.22510.00990.02380.1878-0.01610.2019-29.403155.7074-52.8234
164.1572-0.0408-1.54633.247-1.38732.9707-0.01370.31460.2232-0.26040.07750.1472-0.3232-0.4932-0.05640.23620.03070.03520.22570.00140.1644-48.425963.0758-55.7217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 289:314)
2X-RAY DIFFRACTION2chain 'A' and (resseq 315:395)
3X-RAY DIFFRACTION3chain 'A' and (resseq 396:469)
4X-RAY DIFFRACTION4chain 'A' and (resseq 470:482)
5X-RAY DIFFRACTION5chain 'B' and (resseq 289:314)
6X-RAY DIFFRACTION6chain 'B' and (resseq 315:395)
7X-RAY DIFFRACTION7chain 'B' and (resseq 396:469)
8X-RAY DIFFRACTION8chain 'B' and (resseq 470:482)
9X-RAY DIFFRACTION9chain 'C' and (resseq 289:314)
10X-RAY DIFFRACTION10chain 'C' and (resseq 315:395)
11X-RAY DIFFRACTION11chain 'C' and (resseq 396:469)
12X-RAY DIFFRACTION12chain 'C' and (resseq 470:482)
13X-RAY DIFFRACTION13chain 'D' and (resseq 289:314)
14X-RAY DIFFRACTION14chain 'D' and (resseq 315:395)
15X-RAY DIFFRACTION15chain 'D' and (resseq 396:469)
16X-RAY DIFFRACTION16chain 'D' and (resseq 470:482)

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