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- PDB-7qqd: Nuclear factor one X - NFIX in P21 -

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Basic information

Entry
Database: PDB / ID: 7qqd
TitleNuclear factor one X - NFIX in P21
Components
  • (NFI binding site ...) x 2
  • Nuclear factor 1 X-type
KeywordsDNA BINDING PROTEIN / Transcription Factor / NFI / NFIX / NF-1
Function / homology
Function and homology information


RNA Polymerase III Transcription Termination / RNA Polymerase III Abortive And Retractive Initiation / sequence-specific double-stranded DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA replication / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin ...RNA Polymerase III Transcription Termination / RNA Polymerase III Abortive And Retractive Initiation / sequence-specific double-stranded DNA binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA replication / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
CTF transcription factor/nuclear factor 1 / CTF transcription factor/nuclear factor 1, N-terminal / CTF transcription factor/nuclear factor 1, conserved site / CTF/NF-I family transcription modulation region / Nuclear factor I protein pre-N-terminus / CTF/NF-I DNA-binding domain signature. / CTF transcription factor/nuclear factor 1, DNA-binding domain / CTF/NF-I DNA-binding domain profile. / MAD homology 1, Dwarfin-type / MH1 domain / Domain A in dwarfin family proteins
Similarity search - Domain/homology
DNA / DNA (> 10) / Nuclear factor 1 X-type
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsLapi, M. / Chaves-Sanjuan, A. / Gourlay, L.J. / Tiberi, M. / Polentarutti, M. / Demitri, N. / Bais, G. / Nardini, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Nuclear factor one X - NFIX in P41212
Authors: Lapi, M. / Chaves-Sanjuan, A. / Gourlay, L.J. / Tiberi, M. / Polentarutti, M. / Demitri, N. / Bais, G. / Nardini, M.
History
DepositionJan 7, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear factor 1 X-type
B: Nuclear factor 1 X-type
D: NFI binding site (forward)
F: NFI binding site (reverse)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8359
Polymers48,3354
Non-polymers5005
Water1,13563
1
A: Nuclear factor 1 X-type
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7083
Polymers19,5771
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear factor 1 X-type
D: NFI binding site (forward)
F: NFI binding site (reverse)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1276
Polymers28,7583
Non-polymers3693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.171, 98.358, 61.629
Angle α, β, γ (deg.)90.000, 92.702, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nuclear factor 1 X-type / NF1-X / Nuclear factor 1/X / CCAAT-box-binding transcription factor / CTF / Nuclear factor I/X / NF- ...NF1-X / Nuclear factor 1/X / CCAAT-box-binding transcription factor / CTF / Nuclear factor I/X / NF-I/X / NFI-X / TGGCA-binding protein


Mass: 19577.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GSHM belongs to the expression tag / Source: (gene. exp.) Homo sapiens (human) / Gene: NFIX / Production host: Escherichia coli (E. coli) / References: UniProt: Q14938

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NFI binding site ... , 2 types, 2 molecules DF

#2: DNA chain NFI binding site (forward)


Mass: 4635.011 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain NFI binding site (reverse)


Mass: 4545.949 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 68 molecules

#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 63 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 277 K / Method: microbatch / pH: 7 / Details: 0.2 M NaSCN, 0.1 M HEPES pH 7.0, 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 11.2C / Wavelength: 1.2705 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2705 Å / Relative weight: 1
ReflectionResolution: 2.7→49.18 Å / Num. obs: 14029 / % possible obs: 99.3 % / Redundancy: 6.6 % / Biso Wilson estimate: 66.78 Å2 / CC1/2: 0.968 / Rpim(I) all: 0.054 / Net I/σ(I): 13.2
Reflection shellResolution: 2.7→2.84 Å / Mean I/σ(I) obs: 2 / Num. unique obs: 1374 / CC1/2: 0.817 / Rpim(I) all: 0.559

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Processing

Software
NameVersionClassification
REFMAC5refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XSCALEdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→49.18 Å / SU ML: 0.3036 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.9284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2428 768 5.48 %
Rwork0.195 13258 -
obs0.1979 14026 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 96.93 Å2
Refinement stepCycle: LAST / Resolution: 2.7→49.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2674 615 19 63 3371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00923437
X-RAY DIFFRACTIONf_angle_d1.23074747
X-RAY DIFFRACTIONf_chiral_restr0.0773512
X-RAY DIFFRACTIONf_plane_restr0.0082496
X-RAY DIFFRACTIONf_dihedral_angle_d28.69871401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.910.32241360.26362639X-RAY DIFFRACTION98.72
2.91-3.20.351370.2492648X-RAY DIFFRACTION98.9
3.2-3.660.29021560.21172658X-RAY DIFFRACTION99.05
3.66-4.620.19371640.1752635X-RAY DIFFRACTION99.22
4.62-49.180.23071750.17872678X-RAY DIFFRACTION98.89
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)
13.993277198531.504932565-0.583009706154.86268789608-0.3726991082070.5158950485860.01961124653070.208903129584-0.666879265035-0.387217570547-0.0721907132781-0.1484067882970.06456974540290.1688513903032.49029361284E-70.683670784149-0.00445664262738-0.03524276110790.569498817877-0.1118029288120.6872466641020.1033441071720.917949908588-40.1901047102
26.21354031169-1.20356056911-0.1178438892074.692364644770.2531210703894.97196123073-0.05287955163220.0949529909158-0.180335030326-0.1738847482170.07391845357490.4155466901010.0809175056316-0.3713234510152.24663934447E-80.5002448448580.008204237856290.0003285943535540.4818058795510.02712218574460.549444120263-5.6857272234612.325531056-35.5176330457
32.724599260672.077790268060.5068537977312.01430023516-0.9702000780833.57085144988-0.144304443211-0.618052187784-1.040764072960.3587201066070.277701439272-0.442038944370.241916753439-0.160280755285-0.003288792458410.6186618358110.0551685890787-0.02457486524440.4574594516320.08964387587870.80716514761813.87439784334.78287863935-17.4005905211
44.70841261890.258952775563-0.8880765183671.963381439820.3000447767954.28289181972-0.166183551357-0.416358147147-0.5784828269210.6356718932870.2648192273940.09870261989030.432298579176-0.0567300001425-0.000153716945210.6080299983910.00140815602697-0.01628147987240.557349341459-0.002735112474930.67973492388512.78367754189.8683262318-18.1782355576
51.12587293541-0.202710497183-0.8806573480741.36336190106-0.003795015522771.42221811512-0.341487433154-1.18386176363-0.8503234665290.4049560040560.555935676121-0.892974992617-0.1046887409220.62357869590.002555745313340.6588610131960.0155012404861-0.06816664659430.705498811197-0.06189950786820.73899494716822.988388561213.0157005263-19.8072254475
62.430339659410.5923375732110.2030657491840.693551606103-0.6761210003883.98742850625-0.3127109682770.3293686782970.102974586078-0.5559061236230.432586421262-0.7877517891150.07204379166830.3847473651837.31655170313E-100.5536220046360.01526549281420.0481782950580.543281433458-0.08388413525540.64230670326818.078003025613.3983262334-32.3945735881
70.6723768830220.1061365122120.8075768077090.03797126255390.07722698229990.5107201035040.4898197848821.11593828441-0.241881088034-1.38488910762-1.25323096577-0.6384117470290.9839167387610.50312883563-0.0002289825535592.69507628086-0.189208357499-0.3989252117921.680261695210.04195869095272.3185683624224.92652575926.883832191311.25135654832
80.17538735880.1776276570270.1038826506740.1246796317220.02223033443340.6464857778581.00043026397-1.004617215060.1889735939111.52869069634-0.5216166769150.548119127430.332020720907-1.028670740181.00829721401E-62.594301018940.272236191804-0.4689956791321.661752608880.08793091607012.24491631523.39366960781.157651583812.72738280813
90.0871211206224-0.1121970718790.09186128796610.372046845872-0.1137582628860.09799058866780.0400808702706-0.517086052597-0.001019656162570.2432794184950.8355209778680.0499373769446-0.5011807296970.1514271043570.007252705014883.953923567420.224948934111-0.7644745352891.96014262034-0.7932522395682.1076150849721.101835220526.49483171564.69486906859
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 13 through 96 )AA13 - 961 - 84
22chain 'A' and (resid 97 through 174 )AA97 - 17485 - 162
33chain 'B' and (resid 13 through 43 )BB13 - 431 - 31
44chain 'B' and (resid 44 through 105 )BB44 - 10532 - 93
55chain 'B' and (resid 106 through 137 )BB106 - 13794 - 125
66chain 'B' and (resid 138 through 174 )BB138 - 174126 - 162
77chain 'D' and (resid 2 through 16 )DI2 - 16
88chain 'F' and (resid -16 through -5 )FJ-16 - -5
99chain 'F' and (resid -4 through -2 )FJ-4 - -2

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