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- PDB-7zie: Gcf1p, multimerizes and bridges the mitochondrial DNA from Candid... -

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Basic information

Entry
Database: PDB / ID: 7zie
TitleGcf1p, multimerizes and bridges the mitochondrial DNA from Candida albicans by a specific mechanism.
Components
  • (20-mer DNA) x 2
  • Gcf1p
KeywordsDNA BINDING PROTEIN / Mitochondrial DNA Recombination Compaction
Function / homology
Function and homology information


mitochondrial genome maintenance / mitochondrion / DNA binding / nucleus
Similarity search - Function
HMG boxes A and B DNA-binding domains profile. / high mobility group / High mobility group box domain / High mobility group box domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Gcf1p
Similarity search - Component
Biological speciesCandida albicans (yeast)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SOLUTION SCATTERING / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsTarres-Sole, A. / Sola, M.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)RTI2018-101015-B-100 Spain
Citation
Journal: Nucleic Acids Res. / Year: 2023
Title: Gcf1p tetramerizes upon DNA binding, revealing a novel compaction method for mitochondrial DNA in Candida albicans.
Authors: Tarres-Sole, A. / Ruiz-Lopez, E. / Lyonnais, S. / Sola, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionApr 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 19, 2023Group: Database references / Refinement description / Category: citation / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year / _struct_ncs_dom_lim.beg_auth_asym_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.end_auth_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gcf1p
B: Gcf1p
W: 20-mer DNA
X: 20-mer DNA
Y: 20-mer DNA
Z: 20-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7888
Polymers81,6046
Non-polymers1842
Water25214
1
A: Gcf1p
B: Gcf1p
W: 20-mer DNA
X: 20-mer DNA
Y: 20-mer DNA
Z: 20-mer DNA
hetero molecules

A: Gcf1p
B: Gcf1p
W: 20-mer DNA
X: 20-mer DNA
Y: 20-mer DNA
Z: 20-mer DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,57616
Polymers163,20812
Non-polymers3684
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556x,-y,-z+11
Buried area29180 Å2
ΔGint-144 kcal/mol
Surface area67070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.630, 96.900, 113.060
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y+1/2,-z+1/2
#4: -x,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 60 through 63 or resid 65...
d_2ens_1(chain "B" and (resid 60 through 63 or resid 65...
d_1ens_2chain "W"
d_2ens_2chain "Y"
d_1ens_3(chain "X" and (resid 1 through 18 or resid 20))
d_2ens_3(chain "Z" and (resid 1 through 18 or resid 20))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1THRTHRILEILEAA60 - 6360 - 63
d_12ens_1LEULEUGLNGLNAA65 - 9665 - 96
d_13ens_1PHEPHELYSLYSAA99 - 12199 - 121
d_14ens_1ARGARGTYRTYRAA123 - 132123 - 132
d_15ens_1PHEPHETYRTYRAA134 - 149134 - 149
d_16ens_1GLUGLUGLYGLYAA151 - 179151 - 179
d_17ens_1SERSERLYSLYSAA181 - 187181 - 187
d_18ens_1LEULEUGLNGLNAA189 - 202189 - 202
d_19ens_1TYRTYRGLUGLUAA204 - 242204 - 242
d_21ens_1THRTHRILEILEBB60 - 6360 - 63
d_22ens_1LEULEUGLNGLNBB65 - 9665 - 96
d_23ens_1PHEPHELYSLYSBB99 - 12199 - 121
d_24ens_1ARGARGTYRTYRBB123 - 132123 - 132
d_25ens_1PHEPHETYRTYRBB134 - 149134 - 149
d_26ens_1GLUGLUGLYGLYBB151 - 179151 - 179
d_27ens_1SERSERLYSLYSBB181 - 187181 - 187
d_28ens_1LEULEUGLNGLNBB189 - 202189 - 202
d_29ens_1TYRTYRGLUGLUBB204 - 242204 - 242
d_11ens_2DTDTDTDTWC1 - 201 - 20
d_21ens_2DTDTDTDTYE1 - 201 - 20
d_11ens_3DADADADAXD1 - 201 - 20
d_21ens_3DADADADAZF1 - 201 - 20

NCS ensembles :
ID
ens_1
ens_2
ens_3

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Components

#1: Protein Gcf1p


Mass: 28543.850 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Strain: SC5314 / ATCC MYA-2876 / Gene: GCF1, orf19.400, CAALFM_C108550CA / Plasmid: pGEX-T-4T1
Details (production host): pGEX plasmid containing a TEV cleavage site downstream of the GST-tag
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta2 / References: UniProt: Q59QB8
#2: DNA chain 20-mer DNA


Mass: 6111.011 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain 20-mer DNA


Mass: 6147.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

Experiment
MethodNumber of used crystals
X-RAY DIFFRACTION1
SOLUTION SCATTERING

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 20% PEG 1000 0.1M Na/K-phosphate pH 6.2 0.1M NaCl 3% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.981664, 1.0
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9816641
211
ReflectionResolution: 2.9→73.57 Å / Num. obs: 16672 / % possible obs: 98.57 % / Redundancy: 1.9 % / Biso Wilson estimate: 101.08 Å2 / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.03739 / Net I/σ(I): 10.07
Reflection shellResolution: 2.9→3.004 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 0.76 / Num. unique obs: 1587 / CC1/2: 0.319 / CC star: 0.695 / % possible all: 92.55

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
MxCuBE1.20_4459data collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.9→73.57 Å / SU ML: 0.5136 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.3003
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2631 1656 9.98 %
Rwork0.2112 14933 -
obs0.2164 16589 98.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 124.92 Å2
Refinement stepCycle: LAST / Resolution: 2.9→73.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3104 1628 12 14 4758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00745002
X-RAY DIFFRACTIONf_angle_d0.98847040
X-RAY DIFFRACTIONf_chiral_restr0.0531734
X-RAY DIFFRACTIONf_plane_restr0.007614
X-RAY DIFFRACTIONf_dihedral_angle_d27.41672046
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BX-RAY DIFFRACTIONTorsion NCS1.06931516464
ens_2d_2YX-RAY DIFFRACTIONTorsion NCS0.775323663478
ens_3d_2ZX-RAY DIFFRACTIONTorsion NCS0.831263097097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-2.990.47571280.46561129X-RAY DIFFRACTION92.7
2.99-3.080.42181290.39181204X-RAY DIFFRACTION97.09
3.08-3.190.44711390.34921223X-RAY DIFFRACTION98.55
3.19-3.320.35571380.29091238X-RAY DIFFRACTION99.06
3.32-3.470.32481310.26751228X-RAY DIFFRACTION98.62
3.47-3.650.33031370.23611235X-RAY DIFFRACTION99.78
3.65-3.880.32631400.22281247X-RAY DIFFRACTION99.28
3.88-4.180.30011400.20811256X-RAY DIFFRACTION99.71
4.18-4.60.22851370.17691241X-RAY DIFFRACTION99.57
4.6-5.270.26221420.1981275X-RAY DIFFRACTION99.79
5.27-6.640.26961440.22491295X-RAY DIFFRACTION99.93
6.64-73.570.18741510.16471362X-RAY DIFFRACTION99.61
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)
10.1565867131150.683114785891-0.1617954397541.7580574718-1.145023119862.49874808214-0.2778614073130.191834080072-0.239919929692-0.6822304046150.164815069654-0.2084409729570.6279445931080.4794879521120.1666573405792.08225497399-0.02895885370920.0576403775130.776514524917-0.003506144016080.79541695449477.53997002338.434044873325.8728581192
20.990584366597-0.5110873476381.556906860268.345532036531.68245038752.0411843965-0.2658228007350.09328361872260.278805779354-0.5216765905590.268603913816-0.1901715843780.382194227492-0.1505395366190.004170268922261.83985629129-0.04291758549020.05261491545380.508544500579-0.01720482080010.7247366322470.351188168938.016477339421.6259952744
30.992082949882-0.7088048463121.783445142424.8045036895-1.970382506122.15471456102-0.459733496639-0.3172332083450.3917319338171.453302212130.0363059317269-0.20030821024-0.446762731305-0.3181640538730.3778547386111.718170325440.08693153673810.03189318887570.7057725138350.001534041011160.68822715858988.628168457830.680076944549.2459425013
41.600566021210.491606971784-0.9775926889381.140925891083.547311048949.78972541987-0.1313251412350.193733944037-0.148353657892-0.724257217784-0.196039193949-0.128880721653-0.0618369885338-0.2560956240140.3170496629322.012195076040.0749364271815-0.05599037633270.5533180884140.03710762555410.7712156417696.839856416237.09591617921.5199224975
52.11689424267-9.57410082748-6.092636670151.989619437491.977649287422.034310337781.32711693421.07766431635-2.12641148451.37220247547-2.464998347921.04373978283-0.573669595703-3.91858033381.320357311311.474061221640.211956838455-0.2971139442442.10430204524-0.1443363387451.4263892678980.9028944768-3.4155481769541.0597697053
67.278269146983.70624936244-3.850852022222.43768312444-0.5756303325498.233466369120.526894167963-0.795375792166-0.5733219016222.60657084982-0.1858593208210.15381118808-0.6884968781160.0234726409286-0.3328515644951.366915999620.103306782061-0.05731960856860.808549279750.08370729757670.68643114423489.517229372420.777766376622.9069617136
77.092249112122.69321100273-3.227730907466.10620407428-6.766460838953.250976332970.005597420991-0.4893596368260.323293993612-1.32042677265-0.164500506499-0.009353646540610.948015148810.4524148830380.2066612795581.545218177780.1338674318490.02713596731710.610629007344-0.1039613230620.61034140571887.527891661220.094740663220.3410587313
89.405482590414.175622454354.602013985227.584326980770.2516406996137.24922874654-0.751606077805-0.738095804978-0.738030206552-1.88902975468-0.4037400332540.07177685828111.93048086448-0.3026563299110.8689406418083.100922528470.622457784708-0.2795965658291.10907059879-0.08302328795230.98542514363188.0873098494-2.9632762233242.6168758752
91.96595463009-2.12502686339-0.4124687918819.36714610009-5.009113986797.35583800614-0.504379312532-0.297909626042-0.458511127445-1.331711021281.34488726214-0.0521970727244-0.180301299155-0.0673746413235-0.6817285884781.46756353693-0.2943727570220.1480527230421.222634432340.1783819383421.3360514792379.306960667720.261551557855.530414304
105.49889680187-2.994608205125.915426548559.47074669883-4.580888044448.659720607730.7121539706280.803584364266-0.113551487224-1.92935400203-1.44494376433-1.066935396092.510742596822.301020164630.1959476535221.65221244620.1186437819760.1181386820970.504008665005-0.03391835223110.99704327939678.936930364339.255536201929.7363308497
113.66228236044-3.042439321175.316469697537.52027004516-6.369482664697.849104824970.51953450354-0.437264941098-0.168246687266-0.492076571558-0.525503869910.4271276255571.281658141970.0333037290372-0.09591737439321.40048910033-0.01235695548220.08578807471220.517252629481-0.09947288183830.84405113724679.211733822536.905969884637.9116018234
127.908131930763.295580126672.693849782098.025177934486.828973856662.018819358-1.2492575885-0.0708684382057-0.340576674544-3.790231065111.89225986614-2.03164767402-1.551776688370.568067104438-0.6616068395342.35745399841-0.4971567067290.4200830977281.36599256054-0.07755905871541.0974033761577.021934192713.903808341259.9311405999
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 60 through 156 )AA60 - 1561 - 97
22chain 'A' and (resid 157 through 242 )AA157 - 24298 - 183
33chain 'B' and (resid 60 through 154 )BB60 - 1542 - 96
44chain 'B' and (resid 155 through 243 )BB155 - 24397 - 185
55chain 'W' and (resid 1 through 5 )WC1 - 5
66chain 'W' and (resid 6 through 20 )WC6 - 20
77chain 'X' and (resid 1 through 15 )XD1 - 15
88chain 'X' and (resid 16 through 20 )XD16 - 20
99chain 'Y' and (resid 1 through 10 )YE1 - 10
1010chain 'Y' and (resid 11 through 20 )YE11 - 20
1111chain 'Z' and (resid 1 through 15 )ZF1 - 15
1212chain 'Z' and (resid 16 through 20 )ZF16 - 20

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