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- PDB-5f4h: Archael RuvB-like Holiday junction helicase -

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Basic information

Entry
Database: PDB / ID: 5f4h
TitleArchael RuvB-like Holiday junction helicase
ComponentsNucleotide binding protein PINc
KeywordsHYDROLASE / Helicase / ATPase / Holiday junction
Function / homology
Function and homology information


: / Type II/IV secretion system protein / Type II/IV secretion system protein / 5'-nuclease / Large family of predicted nucleotide-binding domains / PIN domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleotide binding protein PINc
Similarity search - Component
Biological speciesSulfolobus islandicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.699 Å
AuthorsZhai, B. / DuPrez, K.T. / Doukov, T.I. / Shen, Y. / Fan, L.
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structure and Function of a Novel ATPase that Interacts with Holliday Junction Resolvase Hjc and Promotes Branch Migration.
Authors: Zhai, B. / DuPrez, K. / Doukov, T.I. / Li, H. / Huang, M. / Shang, G. / Ni, J. / Gu, L. / Shen, Y. / Fan, L.
History
DepositionDec 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Revision 1.2Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleotide binding protein PINc
B: Nucleotide binding protein PINc
C: Nucleotide binding protein PINc
D: Nucleotide binding protein PINc
E: Nucleotide binding protein PINc
F: Nucleotide binding protein PINc
hetero molecules


Theoretical massNumber of molelcules
Total (without water)346,02738
Polymers343,4116
Non-polymers2,61732
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31950 Å2
ΔGint-52 kcal/mol
Surface area107060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.720, 148.980, 122.130
Angle α, β, γ (deg.)90.000, 104.070, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PROPROAA1 - 4341 - 434
21PROPROBB1 - 4341 - 434
12VALVALAA1 - 4351 - 435
22VALVALCC1 - 4351 - 435
13VALVALAA1 - 4351 - 435
23VALVALDD1 - 4351 - 435
14VALVALAA1 - 4351 - 435
24VALVALEE1 - 4351 - 435
15VALVALAA1 - 4351 - 435
25VALVALFF1 - 4351 - 435
16PROPROBB1 - 4341 - 434
26PROPROCC1 - 4341 - 434
17PROPROBB1 - 4341 - 434
27PROPRODD1 - 4341 - 434
18PROPROBB1 - 4341 - 434
28PROPROEE1 - 4341 - 434
19PROPROBB1 - 4341 - 434
29PROPROFF1 - 4341 - 434
110ASNASNCC1 - 4361 - 436
210ASNASNDD1 - 4361 - 436
111ASNASNCC1 - 4361 - 436
211ASNASNEE1 - 4361 - 436
112ASNASNCC1 - 4361 - 436
212ASNASNFF1 - 4361 - 436
113ASNASNDD1 - 4361 - 436
213ASNASNEE1 - 4361 - 436
114ASNASNDD1 - 4361 - 436
214ASNASNFF1 - 4361 - 436
115ASNASNEE1 - 4361 - 436
215ASNASNFF1 - 4361 - 436

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

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Components

#1: Protein
Nucleotide binding protein PINc


Mass: 57235.121 Da / Num. of mol.: 6 / Mutation: K261A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus islandicus (strain L.S.2.15 / Lassen #1) (archaea)
Strain: L.S.2.15 / Lassen #1 / Gene: LS215_1665 / Production host: Escherichia coli (E. coli) / References: UniProt: C3MQK6
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 3:2 ratio of protein to mother liquor (0.1 M sodium malonate pH 5.0, 12% PEG 3350, 3% glycerol)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.699→39.19 Å / Num. all: 96879 / Num. obs: 89886 / % possible obs: 97.63 % / Redundancy: 7 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 16.1
Reflection shellResolution: 2.699→2.769 Å / Redundancy: 6.6 % / Rmerge(I) obs: 2.453 / Mean I/σ(I) obs: 4.3 / % possible all: 92.67

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Phasing

Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 94618
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
14.63-10033.50.823612
10.35-14.6333.40.8921108
8.45-10.3531.10.9241414
7.32-8.4536.60.881698
6.54-7.3235.60.8641948
5.97-6.5434.40.8682143
5.53-5.9729.20.8942345
5.17-5.5325.80.9022358
4.88-5.1722.10.9162597
4.63-4.8819.70.9342772
4.41-4.6317.90.9412938
4.22-4.41190.9313058
4.06-4.2221.20.9193223
3.91-4.0621.60.8953295
3.78-3.9121.60.8913428
3.66-3.7821.90.8963454
3.55-3.6623.50.8813511
3.45-3.5525.20.8743704
3.36-3.4525.20.8423827
3.27-3.3625.60.8863945
3.19-3.2726.50.8924117
3.12-3.1927.80.8754165
3.05-3.1227.90.874268
2.99-3.0530.20.8654376
2.93-2.9931.20.8584467
2.87-2.9333.70.8334548
2.82-2.8735.70.8084547
2.77-2.8239.50.7634509
2.7-2.7742.40.7376243

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Processing

Software
NameVersionClassification
REFMACrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
Coot0.8.2model building
Blu-Icedata collection
RefinementMethod to determine structure: MAD / Resolution: 2.699→39.19 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2169 / WRfactor Rwork: 0.182 / FOM work R set: 0.6575 / SU B: 48.41 / SU ML: 0.405 / SU R Cruickshank DPI: 0.9767 / SU Rfree: 0.3491 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.977 / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.265 4732 5 %RANDOM
Rwork0.2274 ---
obs0.2293 89886 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 237.43 Å2 / Biso mean: 81.178 Å2 / Biso min: 37.28 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.06 Å2
2---0.11 Å20 Å2
3---0.08 Å2
Refinement stepCycle: final / Resolution: 2.699→39.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19958 0 170 230 20358
Biso mean--92.16 74.98 -
Num. residues----2616
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01920408
X-RAY DIFFRACTIONr_bond_other_d0.0130.0219597
X-RAY DIFFRACTIONr_angle_refined_deg1.9311.98627593
X-RAY DIFFRACTIONr_angle_other_deg2.218345066
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.75852610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33424.596853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.284153532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.44415128
X-RAY DIFFRACTIONr_chiral_restr0.0960.23243
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0222862
X-RAY DIFFRACTIONr_gen_planes_other0.0110.024232
X-RAY DIFFRACTIONr_mcbond_it3.8636.15410458
X-RAY DIFFRACTIONr_mcbond_other3.8636.15410457
X-RAY DIFFRACTIONr_mcangle_it6.2659.22813062
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A431100.19
12B431100.19
21A406420.2
22C406420.2
31A403700.2
32D403700.2
41A435040.18
42E435040.18
51A416180.2
52F416180.2
61B409540.19
62C409540.19
71B409360.2
72D409360.2
81B429140.19
82E429140.19
91B433800.19
92F433800.19
101C394500.2
102D394500.2
111C408200.2
112E408200.2
121C403840.2
122F403840.2
131D407080.2
132E407080.2
141D435660.18
142F435660.18
151E417600.2
152F417600.2
LS refinement shellResolution: 2.699→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.495 331 -
Rwork0.459 6277 -
all-6608 -
obs--92.67 %
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)
11.35060.31290.51730.2405-0.51593.03850.0362-0.14270.0320.124-0.06510.0487-0.2718-0.02690.02890.2734-0.03830.06140.0426-0.00210.2039-95.3346-19.117870.109
22.32021.24410.14931.94510.39843.05340.0844-0.049-0.4527-0.21360.004-0.11390.19280.0016-0.08840.2444-0.00920.07770.01020.02860.2351-92.2186-30.405643.6575
32.66950.0963-0.61380.436-0.52910.8072-0.05430.0959-0.4047-0.0439-0.0563-0.07150.10260.04670.11060.2086-0.02050.02510.0276-0.05160.2218-79.418-21.918838.9833
41.50550.1067-0.33531.3387-0.16312.5171-0.09740.2854-0.0395-0.2941-0.0565-0.2142-0.0590.35440.1540.2075-0.02920.11470.1485-0.04240.2777-66.1058-12.099322.8346
51.51430.46090.24690.9157-0.55032.0609-0.1546-0.1786-0.10290.19910.067-0.163-0.0127-0.21270.08760.2619-0.0226-0.03610.07760.00020.2044-71.001-2.473875.5373
60.59610.18061.04053.49260.33072.82640.0990.0331-0.17710.04850.0048-0.27580.17290.3662-0.10370.1348-0.00590.00140.09890.03450.2567-59.9128-7.395951.0674
70.46920.63770.3711.6359-0.11731.254-0.0774-0.0347-0.0723-0.1734-0.1477-0.35820.27170.27580.22510.16320.14660.05150.13310.04630.4507-51.18522.371237.6905
81.2774-0.2941-0.25421.7597-0.75182.3197-0.06160.3809-0.1096-0.4023-0.1039-0.1221-0.01330.08590.16560.1362-0.03750.04510.1321-0.03910.3361-55.240314.986624.2485
93.1997-2.3291-0.16432.67891.7372.67130.0583-0.14820.61420.1848-0.0096-0.45740.3436-0.2126-0.04870.2665-0.1126-0.14680.08380.10190.4035-72.864926.262774.8864
101.6370.0253-1.93270.26530.18612.46090.1717-0.27440.44760.10840.3316-0.0267-0.06930.5649-0.50320.29230.0328-0.19790.409-0.07620.5155-61.377934.51358.7936
112.0687-1.7546-1.16311.73570.97782.9114-0.11850.0012-0.10460.28810.0472-0.1342-0.33590.35420.07130.2257-0.0205-0.11570.0737-0.00090.3416-60.794827.673449.7247
121.4039-0.19960.17751.3626-1.38051.9016-0.02830.48850.0356-0.1206-0.0424-0.12730.03930.04840.07070.1977-0.0217-0.01480.1733-0.01430.3002-69.437338.224426.0898
132.27541.69463.16992.5833.33025.13360.10710.0509-0.0679-0.4365-0.14470.06-0.2339-0.05580.03760.3754-0.02570.00460.590.06030.2327-69.169241.6751-0.7276
140.1743-0.8767-0.19974.9681.02760.23320.06280.0844-0.0692-0.2706-0.1446-0.0401-0.0904-0.0550.08170.4407-0.0444-0.03220.4982-0.04490.4088-67.257336.5190.7661
152.67672.2186-0.16641.8994-0.10042.894-0.1982-0.26980.3058-0.0571-0.18550.14960.22740.17860.38370.25290.1199-0.1270.0773-0.0240.3882-97.517739.313367.9394
161.1190.9835-1.02861.0921-0.49152.42260.15020.11620.4638-0.0140.16540.34-0.5029-0.0291-0.31560.41620.0444-0.05330.0403-0.00210.332-89.728251.748545.46
172.6688-0.30952.6040.1287-0.49054.0557-0.1915-0.25570.29150.01350.0167-0.1307-0.1662-0.35530.17480.16610.00760.00910.04140.01340.2234-95.461242.415833.4271
181.24360.2226-0.23560.7014-0.98191.864-0.08340.11180.0128-0.0434-0.12830.0070.03840.2550.21170.15330.03650.06340.09320.07750.1622-103.17232.680318.9992
194.46943.29880.50143.2486-0.35740.7084-0.26510.4864-1.1314-0.37510.1485-1.06940.08780.28550.11650.41940.03870.12890.49980.01570.371-100.539823.9995-8.4535
202.6912-1.10581.78714.911-2.00821.84810.00190.32780.0803-0.3909-0.20620.09330.22310.38740.20430.22380.03910.11550.29770.07460.1452-96.799830.6949-2.0933
213.1348-0.6896-2.03191.39661.27043.61220.0216-0.0690.1394-0.10920.0017-0.0924-0.019-0.0457-0.02330.24020.04250.04590.02130.03320.1794-121.946328.043160.5414
220.8501-0.2332-0.88160.9432-0.02321.0641-0.1848-0.0658-0.08390.24570.0992-0.02620.1454-0.00110.08560.25460.04050.0730.04370.0080.1892-125.775220.137559.5258
230.8123-0.4122-0.62772.87090.05061.4080.06530.05750.1466-0.0587-0.1275-0.115-0.0829-0.24650.06220.19950.04080.08110.07250.00750.1499-121.040328.385735.2617
241.17250.0323-0.12141.3342-0.04710.7339-0.07090.3095-0.0138-0.1152-0.01470.25060.2344-0.05520.08560.2268-0.01320.05160.14090.02070.104-123.859613.355916.579
251.7954-0.71720.4662.2537-0.49943.16590.06880.3052-0.0735-0.3404-0.2154-0.31330.44290.24010.14660.28180.01440.11630.0954-0.02950.1521-113.74846.093914.7559
260.5062-1.21461.00543.0104-2.39182.06720.09040.01340.0213-0.2034-0.12-0.00970.38820.01890.02960.5109-0.01450.07340.3668-0.10790.2289-110.96251.1218-9.775
271.89351.7271-0.51994.82840.34330.3924-0.12540.032-0.5130.00210.001-0.78660.20910.06320.12440.55820.13540.23490.6369-0.01420.2689-110.26014.633-7.8586
282.11550.7447-0.44211.3556-0.66422.31550.077-0.0093-0.20080.10210.17220.34110.0307-0.0783-0.24910.24030.02760.0620.059-0.01010.3904-121.7454-6.006561.8234
295.2303-0.24510.09962.5312-0.04953.3166-0.03250.1553-0.1577-0.0109-0.05120.0070.2874-0.07570.08370.1614-0.00740.08310.10550.02470.1713-122.8048-7.033334.6527
301.358-1.6253-1.12692.9931.08041.0833-0.1270.1542-0.1340.15710.01440.21670.1236-0.06930.11260.2204-0.0160.0060.2423-0.08060.2171-110.8432-17.452922.877
311.2088-0.1025-0.2750.65960.90512.5610.01880.2938-0.0555-0.1505-0.0067-0.0931-0.3868-0.0816-0.01210.273-0.01650.05320.0754-0.02620.1834-93.8576-16.114117.1375
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 127
2X-RAY DIFFRACTION2A128 - 184
3X-RAY DIFFRACTION3A185 - 245
4X-RAY DIFFRACTION4A246 - 437
5X-RAY DIFFRACTION5B1 - 126
6X-RAY DIFFRACTION6B127 - 210
7X-RAY DIFFRACTION7B211 - 244
8X-RAY DIFFRACTION8B245 - 435
9X-RAY DIFFRACTION9C1 - 111
10X-RAY DIFFRACTION10C112 - 141
11X-RAY DIFFRACTION11C142 - 210
12X-RAY DIFFRACTION12C211 - 384
13X-RAY DIFFRACTION13C385 - 404
14X-RAY DIFFRACTION14C415 - 436
15X-RAY DIFFRACTION15D1 - 110
16X-RAY DIFFRACTION16D111 - 167
17X-RAY DIFFRACTION17D168 - 248
18X-RAY DIFFRACTION18D249 - 388
19X-RAY DIFFRACTION19D389 - 408
20X-RAY DIFFRACTION20D409 - 437
21X-RAY DIFFRACTION21E1 - 65
22X-RAY DIFFRACTION22E66 - 134
23X-RAY DIFFRACTION23E135 - 210
24X-RAY DIFFRACTION24E211 - 284
25X-RAY DIFFRACTION25E285 - 384
26X-RAY DIFFRACTION26E385 - 404
27X-RAY DIFFRACTION27E405 - 436
28X-RAY DIFFRACTION28F1 - 127
29X-RAY DIFFRACTION29F128 - 210
30X-RAY DIFFRACTION30F211 - 245
31X-RAY DIFFRACTION31F246 - 436

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