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- PDB-5dzm: HIV-1 Reverse Transcriptase RH domain -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5dzm
TitleHIV-1 Reverse Transcriptase RH domain
ComponentsRibonuclease H
KeywordsHYDROLASE / HIV / ribonuclease / unfolding / reverse transcriptase
Function / homology
Function and homology information


ribonuclease H / DNA integration / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / peptidase activity / nucleic acid binding / proteolysis
Similarity search - Function
RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Ribonuclease H superfamily / Ribonuclease H-like superfamily
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsPedersen, L.C. / London, R.E. / Gabel, S.A. / Zheng, X.H.
CitationJournal: Nucleic Acids Res. / Year: 2016
Title: Unfolding the HIV-1 reverse transcriptase RNase H domain - how to lose a molecular tug-of-war.
Authors: Zheng, X. / Pedersen, L.C. / Gabel, S.A. / Mueller, G.A. / DeRose, E.F. / London, R.E.
History
DepositionSep 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribonuclease H
D: Ribonuclease H
C: Ribonuclease H
B: Ribonuclease H


Theoretical massNumber of molelcules
Total (without water)61,1054
Polymers61,1054
Non-polymers00
Water4,053225
1
A: Ribonuclease H


Theoretical massNumber of molelcules
Total (without water)15,2761
Polymers15,2761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Ribonuclease H


Theoretical massNumber of molelcules
Total (without water)15,2761
Polymers15,2761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Ribonuclease H


Theoretical massNumber of molelcules
Total (without water)15,2761
Polymers15,2761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
B: Ribonuclease H


Theoretical massNumber of molelcules
Total (without water)15,2761
Polymers15,2761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Ribonuclease H
B: Ribonuclease H


Theoretical massNumber of molelcules
Total (without water)30,5532
Polymers30,5532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-42 kcal/mol
Surface area12440 Å2
MethodPISA
6
D: Ribonuclease H
C: Ribonuclease H


Theoretical massNumber of molelcules
Total (without water)30,5532
Polymers30,5532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-42 kcal/mol
Surface area12450 Å2
MethodPISA
7


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14780 Å2
ΔGint-109 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.140, 56.140, 133.749
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsThis molecule in its biological context is the C-terminal domain of the HIV RT protein. It can run as either a monomer or dimer on gel filtration. In the crystal structure it has formed a domain-swapped dimer with the C-terminal helix-strand swapping between two monomers. In the crystal structure two domain-swapped dimers come together to form what looks like a tetramer.

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Components

#1: Protein
Ribonuclease H


Mass: 15276.277 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7LYY8, ribonuclease H
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / 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: 1.99 Å3/Da / Density % sol: 38.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M ammonium acetate, 0.1M Bis-Tris pH 5.5, 17% PEG 10,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 29211 / Num. obs: 29211 / % possible obs: 98.3 % / Redundancy: 5.3 % / Rsym value: 0.053 / Net I/σ(I): 10.8
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.6 / % possible all: 79.6

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
DENZOdata reduction
PHENIXphasing
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3K2P
Resolution: 2.05→48.619 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 2.19 / Phase error: 23.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2248 1415 5.05 %Random
Rwork0.1779 ---
obs0.1803 28005 94.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→48.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3424 0 0 225 3649
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043537
X-RAY DIFFRACTIONf_angle_d0.8244837
X-RAY DIFFRACTIONf_dihedral_angle_d14.1241265
X-RAY DIFFRACTIONf_chiral_restr0.049581
X-RAY DIFFRACTIONf_plane_restr0.003632
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0487-2.12190.3104940.22381548X-RAY DIFFRACTION55
2.1219-2.20690.26121320.22072517X-RAY DIFFRACTION90
2.2069-2.30730.29481460.19792825X-RAY DIFFRACTION100
2.3073-2.4290.24151520.18952837X-RAY DIFFRACTION100
2.429-2.58120.21741440.18832808X-RAY DIFFRACTION100
2.5812-2.78040.27731540.20222804X-RAY DIFFRACTION100
2.7804-3.06020.24241470.19942808X-RAY DIFFRACTION100
3.0602-3.50290.22891490.17352840X-RAY DIFFRACTION100
3.5029-4.41280.18981530.14162795X-RAY DIFFRACTION100
4.4128-48.63230.18381440.16682808X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.6469-0.93481.55273.3882-1.25716.05830.25030.54890.2967-0.10550.06470.3038-0.3929-0.1932-0.25840.22040.06210.03830.14890.06530.2858-59.815358.08761.7463
25.1842-3.2845-3.57292.90252.13014.2596-0.0178-0.35820.29310.05240.2046-0.24290.13340.2437-0.15050.19410.0680.04830.12170.03980.1536-50.499547.479612.7592
30.60790.21410.35010.15110.0960.2113-0.0295-0.25390.0217-0.00920.077-0.08490.03030.386-0.12080.63190.17110.6720.81990.0751.0531-29.090343.7717-1.3949
43.5801-0.6753-1.34481.75141.13432.8667-0.1267-0.00420.0063-0.28460.3227-0.46680.07790.2767-0.05610.28110.06150.1360.15130.02290.2083-45.434239.73738.674
55.1112.0755-3.29381.4277-2.40446.9554-0.41950.206-0.7671-0.4198-0.0963-0.50930.67860.20850.49410.562-0.0670.43230.38610.11010.7384-35.979745.9655-3.3268
64.574-0.71-2.60394.8052-1.77225.0181-0.0780.551-0.2896-0.60140.2851-0.68040.19370.3533-0.24780.2507-0.00170.07040.1582-0.07230.2152-44.745347.14191.5898
73.32241.6179-0.42523.414-0.4863.3131-0.11270.17230.0474-0.10840.31770.0785-0.01460.2419-0.20970.12470.01080.0270.0858-0.01720.1138-49.687851.77745.6274
87.71263.247-5.32129.2324-5.04874.7828-0.0055-0.1429-0.11640.3549-0.09940.54380.255-0.30220.07740.2061-0.05020.03390.34650.12160.2956-50.996563.6446-8.8125
97.56070.1617-6.25664.36360.00086.9497-0.39510.147-0.7295-0.48350.150.00750.7504-0.4030.20750.2086-0.02090.00080.21030.06660.1875-37.726865.0719-19.0511
103.1409-1.138-1.46632.36990.93637.5303-0.2236-0.18020.07950.0418-0.1436-0.0254-0.0499-0.07530.24450.10360.0514-0.01490.24670.05070.1282-28.198571.4121-8.2647
114.47980.7874-2.40980.7646-0.80791.5306-0.3036-0.0941-0.97250.08630.1227-0.20910.24190.26440.23090.16170.15230.09460.54840.1360.3448-25.432566.0068-15.7528
123.58221.30682.15791.9799-0.93793.27880.01530.06770.02090.0169-0.007-0.0154-0.1199-0.08730.020.1736-0.0129-0.01880.44490.21320.1943-24.295476.2426-22.6615
134.38261.0758-4.15753.50480.13834.3946-0.0149-0.88830.31320.6778-0.12090.184-0.8276-0.2118-0.14160.32340.0915-0.06210.4423-0.02950.1417-37.486779.3083-8.0103
144.4907-0.718-2.46432.00911.34723.56-0.0668-0.43240.3586-0.0237-0.15580.279-1.0063-0.57420.03390.30810.1282-0.07080.3767-0.0210.1915-41.207982.1145-12.3231
155.40080.3717-0.99893.34740.31561.6538-0.1041-0.82050.10370.29860.16810.4608-0.0869-0.90880.0357-0.01060.1924-0.01620.76550.09190.1938-44.623973.7515-6.6019
161.94550.64710.55530.86950.86492.2711-0.0723-0.15150.0354-0.15120.00930.019-0.3814-0.27470.13290.03720.0227-0.01520.17720.06390.1086-34.390273.5578-18.4307
179.33425.31973.32816.37173.44546.69450.268-0.76480.34320.27490.12860.01460.2942-0.131-0.33060.15440.0725-0.03080.39210.02810.236-36.184968.9958-3.8191
185.05984.23872.64364.96342.39682.2713-0.88430.9809-0.2058-0.46520.3972-0.38110.6048-0.22770.41770.5199-0.11940.06350.5340.09060.2989-40.782655.0818-8.4626
197.8127-0.2478-0.00572.193-0.59462.9447-0.32810.9794-0.672-0.74050.2969-0.04330.26950.1380.09110.3999-0.10880.01610.2084-0.0380.1979-51.781749.417-5.0416
203.1611.10820.3793.560.26022.2985-0.03880.0159-0.2087-0.04130.18450.1151-0.1206-0.1204-0.15060.11680.02180.0290.03340.02980.1212-54.242953.09037.9707
213.08240.18680.74663.80522.12164.91760.242-0.23870.41650.40680.02830.1453-0.8582-0.6729-0.10970.26760.0610.12020.1723-0.00520.2805-20.551180.84194.6705
220.7986-0.5451-0.26825.531-3.89964.69350.05360.1202-0.0492-0.38440.18160.31430.276-0.0376-0.17570.20480.06510.05010.12460.0350.1597-15.860367.4705-6.1079
231.66490.81310.76492.8472-1.66032.7729-0.02060.15350.1183-0.05820.06780.0974-0.16720.027-0.09170.9373-0.14750.46490.81490.44990.878-23.823346.58637.6735
243.532-0.62240.53682.5755-0.46073.49290.2774-0.2049-0.4971-0.12630.03780.16160.4119-0.05730.37910.14660.22240.10610.04260.01660.1669-12.273160.5804-3.8845
255.01724.9908-6.14095.1105-6.52778.78010.0058-0.6061-0.7520.10990.24360.37210.1964-0.2749-0.13530.20890.08710.05170.25540.11040.3038-11.232256.04381.1161
264.57871.5236-3.35261.6807-1.08443.1406-0.2636-0.6285-0.64290.0611-0.0613-0.28730.50170.34720.37590.41560.07670.25610.46840.36750.6669-20.536753.90469.9044
276.49291.653-0.95317.08220.25014.46960.2163-0.7378-0.54870.3375-0.1928-0.14630.465-0.0346-0.09160.20010.066-0.01780.23190.08890.1919-18.414462.31155.0425
283.63380.692-0.42871.5-0.21172.94880.254-0.3239-0.0094-0.0512-0.0798-0.06430.1362-0.1569-0.17440.08580.03080.00610.12330.0390.1403-20.205969.17711.5253
296.76185.8888-6.7677.347-6.93487.70770.2147-0.5464-0.0662-0.0003-0.4135-0.6401-0.33890.7810.12560.2244-0.04720.07490.2556-0.0680.2292-33.599670.891620.9235
302.11050.9227-0.00222.55732.39732.6517-0.2389-0.1116-0.1488-0.0393-0.1621-0.2550.4214-0.10810.1250.2325-0.0180.07380.084-0.01050.1669-46.185659.667719.6835
315.80581.3836-0.93152.52820.20991.95850.04530.1075-0.5379-0.3915-0.2141-0.51220.96170.05530.14360.6055-0.00220.20210.1999-0.00480.2968-44.815454.941222.3032
320.9118-0.01110.00431.5758-2.37664.4025-0.0374-0.0494-0.086-0.0833-0.09290.14850.4346-0.21330.0760.3799-0.22360.12610.2825-0.29110.0712-53.811660.047928.3568
335.00070.8875-2.43483.5812-4.60576.3519-0.29370.77350.3545-0.89170.07950.2019-0.6216-0.5604-0.23330.547-0.0336-0.06840.2897-0.03560.1379-49.970272.099614.6538
343.26542.0019-2.7856.2135-5.54348.4417-0.35830.28240.3301-0.26680.32190.5152-0.7668-0.8999-0.17390.35810.0285-0.09470.2544-0.06470.1688-51.902874.919219.1652
352.06750.3881.09813.2477-1.04491.5504-0.32030.32780.4928-0.5870.432-0.0508-1.05050.0774-0.11110.633-0.09140.03190.15650.00050.2414-43.451477.390515.0159
362.35151.09651.54422.06020.55192.6789-0.1558-0.1368-0.080.04230.0555-0.0283-0.4517-0.12650.14730.1619-0.05810.04990.0701-0.05280.1023-46.495866.564525.1007
372.06371.46062.97863.9960.47486.2081-0.07850.5309-0.1543-0.58560.40510.0926-0.12810.5056-0.32430.4061-0.1050.05660.2176-0.05230.2287-40.386165.052110.895
386.1036-0.63214.70412.0189-3.21237.4349-0.0907-0.9797-0.75130.5925-0.39350.19820.2479-0.15070.34310.4067-0.03790.10680.64420.10050.4477-24.942463.426215.8842
395.46065.0067-1.54115.0969-0.53194.05320.1538-1.4008-0.45990.781-0.3149-0.08570.1330.39610.07850.2139-0.01290.01290.58940.04050.2007-18.231867.904513.2405
404.66330.17960.95461.4953-0.12553.83680.1211-0.2496-0.1366-0.1580.0932-0.1605-0.0906-0.0555-0.25780.07610.06660.03180.11280.00740.1189-18.35572.94330.5716
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 423:432)
2X-RAY DIFFRACTION2(chain A and resid 433:446)
3X-RAY DIFFRACTION3(chain A and resid 447:451)
4X-RAY DIFFRACTION4(chain A and resid 452:470)
5X-RAY DIFFRACTION5(chain A and resid 471:474)
6X-RAY DIFFRACTION6(chain A and resid 475:484)
7X-RAY DIFFRACTION7(chain A and resid 485:508)
8X-RAY DIFFRACTION8(chain A and resid 509:516)
9X-RAY DIFFRACTION9(chain A and resid 517:530)
10X-RAY DIFFRACTION10(chain A and resid 531:537)
11X-RAY DIFFRACTION11(chain B and resid 426:434)
12X-RAY DIFFRACTION12(chain B and resid 436:437)
13X-RAY DIFFRACTION13(chain B and resid 439:448)
14X-RAY DIFFRACTION14(chain B and resid 449:470)
15X-RAY DIFFRACTION15(chain B and resid 471:482)
16X-RAY DIFFRACTION16(chain B and resid 483:497)
17X-RAY DIFFRACTION17(chain B and resid 498:506)
18X-RAY DIFFRACTION18(chain B and resid 507:514)
19X-RAY DIFFRACTION19(chain B and resid 515:524)
20X-RAY DIFFRACTION20(chain B and resid 525:538)
21X-RAY DIFFRACTION21(chain C and resid 423:432)
22X-RAY DIFFRACTION22(chain C and resid 433:446)
23X-RAY DIFFRACTION23(chain C and resid 447:450)
24X-RAY DIFFRACTION24(chain C and resid 451:463)
25X-RAY DIFFRACTION25(chain C and resid 464:469)
26X-RAY DIFFRACTION26(chain C and resid 470:474)
27X-RAY DIFFRACTION27(chain C and resid 475:484)
28X-RAY DIFFRACTION28(chain C and resid 485:509)
29X-RAY DIFFRACTION29(chain C and resid 510:527)
30X-RAY DIFFRACTION30(chain C and resid 528:537)
31X-RAY DIFFRACTION31(chain D and resid 427:434)
32X-RAY DIFFRACTION32(chain D and resid 435:438)
33X-RAY DIFFRACTION33(chain D and resid 439:448)
34X-RAY DIFFRACTION34(chain D and resid 449:464)
35X-RAY DIFFRACTION35(chain D and resid 465:482)
36X-RAY DIFFRACTION36(chain D and resid 483:497)
37X-RAY DIFFRACTION37(chain D and resid 498:508)
38X-RAY DIFFRACTION38(chain D and resid 509:514)
39X-RAY DIFFRACTION39(chain D and resid 515:520)
40X-RAY DIFFRACTION40(chain D and resid 521:538)

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