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- PDB-6guu: Structure of CHD5 PHD2 - tandem chromodomains -

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Basic information

Entry
Database: PDB / ID: 6guu
TitleStructure of CHD5 PHD2 - tandem chromodomains
ComponentsChromodomain-helicase-DNA-binding protein 5
KeywordsDNA BINDING PROTEIN / CHD5 / chromodomain / chromatin remodelling
Function / homology
Function and homology information


sperm DNA condensation => GO:0035092 / H3K27me3 modified histone binding / : / ATP-dependent chromatin remodeler activity => GO:0140658 / : / cerebral cortex neuron differentiation / NuRD complex / positive regulation of signal transduction by p53 class mediator / heterochromatin / DNA helicase activity ...sperm DNA condensation => GO:0035092 / H3K27me3 modified histone binding / : / ATP-dependent chromatin remodeler activity => GO:0140658 / : / cerebral cortex neuron differentiation / NuRD complex / positive regulation of signal transduction by p53 class mediator / heterochromatin / DNA helicase activity / DNA helicase / hydrolase activity / nuclear speck / negative regulation of cell population proliferation / regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / membrane / metal ion binding / nucleus / cytosol
Similarity search - Function
Chromodomain-helicase-DNA-binding protein 5 / CHD subfamily II, SANT-like domain / Domain of unknown function DUF1087 / CHD, C-terminal 2 / CHD, N-terminal / CHD subfamily II, SANT-like domain / CHD subfamily II, DUF1087 / CHDNT (NUC034) domain / CHDCT2 (NUC038) domain / Domain of Unknown Function (DUF1086) ...Chromodomain-helicase-DNA-binding protein 5 / CHD subfamily II, SANT-like domain / Domain of unknown function DUF1087 / CHD, C-terminal 2 / CHD, N-terminal / CHD subfamily II, SANT-like domain / CHD subfamily II, DUF1087 / CHDNT (NUC034) domain / CHDCT2 (NUC038) domain / Domain of Unknown Function (DUF1086) / DUF1087 / Chromo domain / Chromo (CHRromatin Organisation MOdifier) domain / Chromo and chromo shadow domain profile. / Chromo/chromo shadow domain / Chromatin organization modifier domain / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / DNA/RNA helicase, ATP-dependent, DEAH-box type, conserved site / DEAH-box subfamily ATP-dependent helicases signature. / Chromo-like domain superfamily / Zinc finger, PHD-type, conserved site / PHD-finger / Zinc finger PHD-type signature. / Zinc finger PHD-type profile. / Zinc finger, PHD-finger / Helicase conserved C-terminal domain / Zinc finger, PHD-type / PHD zinc finger / Zinc finger, FYVE/PHD-type / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chromodomain-helicase-DNA-binding protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsAlt, A. / Mancini, E.J.
CitationJournal: To Be Published
Title: Structure of CHD5 PHD2 - tandem chromodomains
Authors: Alt, A. / Mancini, E.J.
History
DepositionJun 19, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 9, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: 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: Chromodomain-helicase-DNA-binding protein 5
B: Chromodomain-helicase-DNA-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4336
Polymers57,1712
Non-polymers2624
Water0
1
A: Chromodomain-helicase-DNA-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7173
Polymers28,5861
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chromodomain-helicase-DNA-binding protein 5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7173
Polymers28,5861
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)131.628, 131.628, 84.569
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Chromodomain-helicase-DNA-binding protein 5 / CHD-5 / ATP-dependent helicase CHD5


Mass: 28585.719 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHD5, KIAA0444 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDI0, DNA helicase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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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: 3.8 Å3/Da / Density % sol: 67.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium nitrate 20 % PEG 3350 2 % benzamidine hydrochloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97265 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97265 Å / Relative weight: 1
ReflectionResolution: 2.95→51.94 Å / Num. obs: 16801 / % possible obs: 99.96 % / Redundancy: 2 % / Biso Wilson estimate: 102.23 Å2 / Rmerge(I) obs: 0.02487 / Rrim(I) all: 0.03517 / Rsym value: 0.02487 / Net I/σ(I): 17.18
Reflection shellResolution: 2.95→3.056 Å / Rmerge(I) obs: 0.5412 / Rrim(I) all: 0.7654 / Rsym value: 0.5412

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Processing

Software
NameVersionClassification
REFMAC1.13_2998refinement
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O9I

4o9i


Resolution: 2.95→51.94 Å / SU ML: 0.4745 / Cross valid method: FREE R-VALUE / σ(F): 0.79 / Phase error: 29.2781
RfactorNum. reflection% reflection
Rfree0.263 1538 5.15 %
Rwork0.2063 --
obs0.2091 16166 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 117.22 Å2
Refinement stepCycle: LAST / Resolution: 2.95→51.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3390 0 4 0 3394
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043521
X-RAY DIFFRACTIONf_angle_d0.68564787
X-RAY DIFFRACTIONf_chiral_restr0.0423457
X-RAY DIFFRACTIONf_plane_restr0.0047610
X-RAY DIFFRACTIONf_dihedral_angle_d8.44662072
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.95-3.050.40231420.35722558X-RAY DIFFRACTION100
3.05-3.150.35011600.32822571X-RAY DIFFRACTION100
3.15-3.280.31210.27812575X-RAY DIFFRACTION100
3.28-3.430.30761560.26542561X-RAY DIFFRACTION100
3.43-3.610.25881290.22792584X-RAY DIFFRACTION99.96
3.61-3.840.23441420.20412605X-RAY DIFFRACTION100
3.84-4.130.27531130.19372600X-RAY DIFFRACTION100
4.13-4.550.19411420.16492566X-RAY DIFFRACTION100
4.55-5.210.23471680.16162547X-RAY DIFFRACTION100
5.21-6.560.25251200.20642603X-RAY DIFFRACTION100
6.56-51.950.29321450.20622575X-RAY DIFFRACTION99.93
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)
11.73478411889-1.11513080621-1.927749336815.67951123996-1.790914164088.21936966076-1.15641048898-0.416570174098-1.456765375991.297629435470.2930762703870.1678652861570.7611077269660.1462180147290.8702137226481.320150380160.06341516221640.2118642997380.587190151862-0.008580398964131.29518089499165.159178894141.057734691100.272737275
22.092700148122.1146495767-0.1363213520415.91686786175-2.571266611123.60684997324-0.210062908190.136584897729-2.142864407250.6916150489820.266675659051.377706476130.531568852774-0.008111251567530.4036861358981.126480510440.02865615884680.04220915158360.7320479801280.0728258472241.67879428285156.350709512138.26488009798.7758617471
37.95498419392-2.662143677320.7377642748057.353084616812.11145017994.088572901150.112511288344-1.10789653415-0.417441487431.334626977870.8703274194960.0367647270243-0.485199341335-0.445269342805-0.7923714491421.04648852742-0.04392098860570.1912640900550.691017136660.1948423464551.02126235227144.849068584157.857252584104.543418762
44.94701443401-2.845822849310.7917094005935.261743751910.8757338503970.524882821612-0.29551144939-0.590730370659-0.7998040002210.530028682935-0.168873781801-1.036713198010.600145484371-0.4344003616780.5545581213611.18429823230.06309366712070.372925078080.8630409558310.2884981790111.11071882509141.198701804155.23490716105.468248024
55.56058941917-1.37535031661-0.8314474529814.783020208491.623251993423.590604402770.05766025498730.397171653088-0.0820598371070.8386846700910.354175663144-0.2635496661850.156967699444-0.0865516127015-0.196250376181.156875396810.06985870925410.1258673354370.6235425764980.1021162667420.844409212356151.448474579157.525103938105.204468167
62.64939302197-2.10673829355-1.087834080353.455594879391.230749054012.3054024743-0.596661723845-0.659750160458-0.1931160454440.4174272750960.2952722348340.4886342143340.1469605828520.08889898404230.5422662460691.308814894880.1664168439660.3646003272351.096298313830.2443171175520.929484194706135.786202623162.755189883114.469744416
75.54011571355-0.5355365534370.7453811152455.278395589180.811147636316.587861460780.17233477195-0.0306596442785-0.2244347236260.883243880223-0.1306790806920.7235888182970.580408193506-0.068556279933-0.203421386550.7515196994190.1102208395830.2205033800130.725353537960.04837193037840.80020393799129.879700815173.5384719192.6988740634
89.151056471752.07618931358-1.146314305034.299987686550.5042087400338.36094338239-0.545626112924-0.657150549651-1.079438607220.0161405301950.0562572770998-0.601983405793-0.5043822185390.4085889788020.3822038144040.9852469308180.06473338895060.2051314135920.6422090198130.2154303370481.00923458486131.403943165172.71789762199.8801317773
91.93925664669-0.5787327771790.03306568829462.22637554384-2.07526477518.82759698190.00576548058261-0.43102087688-1.61003123654-0.274687605638-0.4798107492050.33886872359-0.101956579611-1.003534696340.2266807170120.833663591831-0.02705775613590.1625593802721.247199170430.02866679202861.00686051866120.93272538176.4481853694.4811066677
109.11239131437-3.105031595274.492769585792.14295820211-2.798265285466.387977442520.2408697457840.1625811473540.363315230968-0.454710576915-0.629062278823-0.3400181442240.6203210909-0.273468620990.2189541211930.9288983925380.1200103414520.09545091643261.28139995954-0.1681395341511.07764058929168.497676067163.66467378162.1445401195
114.92257353246-2.35920741365-0.1066427327932.91349938163-1.314833355542.224634704550.8091095285371.881069523641.23778631973-0.652491438864-0.332686086057-2.34954444796-0.110293019250.2290743787160.03207374635810.857445739529-0.0677472869870.1818104657991.342010869320.07662020514491.02108915633173.847651693170.68785796965.3190024741
124.0056174506-2.89959848074-1.857351136194.698819163773.133441375813.602207934610.1128347508110.4824618568310.193208129524-0.4325661194270.072111646645-0.138422228263-0.712011458261-0.0801828419078-0.1291177988920.81374973498-0.08755308410210.08471227449120.9005240289010.1967375013010.813054898737152.960840997184.88655115574.0206553986
135.129178654452.53549265742.142823784287.15126043155-1.157446741097.376972163820.02976714327560.03352663362790.1286434663710.122293579007-0.0677772845688-0.0959463182253-0.1625774166450.217589778532-0.07662110398620.759361396223-0.008661639919240.0949859645110.725203392170.07838795361050.716188566535145.659057316188.31353637995.5747561573
143.40950686272-4.94797232882-1.322217207949.628550206356.583246512199.63901173975-0.540360854279-1.37720970894-0.107555911180.1458025838020.4970965603270.2956161212730.245109650517-0.1309622402020.2614369958490.861718435884-0.0141643996189-0.04595272403511.061508904260.1216840439411.03163015822142.353576602194.117425635106.221108637
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 413 through 432 )
2X-RAY DIFFRACTION2chain 'A' and (resid 433 through 461 )
3X-RAY DIFFRACTION3chain 'A' and (resid 462 through 477 )
4X-RAY DIFFRACTION4chain 'A' and (resid 478 through 523 )
5X-RAY DIFFRACTION5chain 'A' and (resid 524 through 545 )
6X-RAY DIFFRACTION6chain 'A' and (resid 546 through 592 )
7X-RAY DIFFRACTION7chain 'A' and (resid 593 through 614 )
8X-RAY DIFFRACTION8chain 'A' and (resid 615 through 633 )
9X-RAY DIFFRACTION9chain 'A' and (resid 634 through 643 )
10X-RAY DIFFRACTION10chain 'B' and (resid 413 through 432 )
11X-RAY DIFFRACTION11chain 'B' and (resid 433 through 457 )
12X-RAY DIFFRACTION12chain 'B' and (resid 458 through 592 )
13X-RAY DIFFRACTION13chain 'B' and (resid 593 through 633 )
14X-RAY DIFFRACTION14chain 'B' and (resid 634 through 649 )

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