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- PDB-3ga1: Crystal Structure of the Human Nac1 POZ Domain -

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Basic information

Entry
Database: PDB / ID: 3ga1
TitleCrystal Structure of the Human Nac1 POZ Domain
ComponentsNucleus accumbens-associated protein 1
KeywordsTRANSCRIPTION / BTB/POZ domain / Nucleus / Phosphoprotein / Repressor / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription repressor activity, RNA polymerase II-specific / histone deacetylase binding / cell junction / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
BEN domain / BEN domain / BEN domain profile. / BEN / : / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac ...BEN domain / BEN domain / BEN domain profile. / BEN / : / Potassium Channel Kv1.1; Chain A / Potassium Channel Kv1.1; Chain A / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Nucleus accumbens-associated protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsStead, M.A. / Carr, S.B. / Wright, S.C.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of the human Nac1 POZ domain
Authors: Stead, M.A. / Carr, S.B. / Wright, S.C.
History
DepositionFeb 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleus accumbens-associated protein 1
B: Nucleus accumbens-associated protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7896
Polymers28,5402
Non-polymers2484
Water1,928107
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4450 Å2
ΔGint-27 kcal/mol
Surface area12540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.690, 57.690, 172.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Nucleus accumbens-associated protein 1 / BTB/POZ domain-containing protein 14B / Nucleus accumbens-1 / NAC-1


Mass: 14270.242 Da / Num. of mol.: 2 / Fragment: POZ Domain, UNP residues 2-125 / Mutation: F98D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAC1 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pLysS / References: UniProt: Q96RE7
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.52 Å3/Da / Density % sol: 51.11 % / Mosaicity: 0.477 °
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 6M ammonium nitrate, 0.1M bis-tris propane, pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 21, 2009 / Details: Mirrors
RadiationMonochromator: Sigitally Focussed Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionRedundancy: 6.75 % / Number: 120991 / Rmerge(I) obs: 0.103 / D res high: 2.1 Å / D res low: 47.96 Å
ReflectionResolution: 2.1→47.96 Å / Num. obs: 17928 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 26.855 Å2 / Rmerge(I) obs: 0.103 / Rsym value: 0.111 / Net I/σ(I): 13.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 7 % / Rmerge(I) obs: 0.506 / Mean I/σ(I) obs: 4 / Num. measured all: 17832 / Num. unique all: 2542 / Rsym value: 0.546 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 56.87 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.96 Å
Translation2.5 Å47.96 Å

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Processing

Software
NameVersionClassificationNB
SCALACCP4_3.3.9 2008/10/21data scaling
ADSCQuantumdata collection
MOSFLMdata reduction
PHASERphasing
REFMAC5.5.0066refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IF5

2if5


Resolution: 2.1→47.96 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.243 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.854 / SU B: 9.577 / SU ML: 0.118 / SU R Cruickshank DPI: 0.206 / SU Rfree: 0.176 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.206 / ESU R Free: 0.176 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.241 908 5.1 %RANDOM
Rwork0.206 ---
obs0.208 17862 99.97 %-
all-16954 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 55.26 Å2 / Biso mean: 18.089 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2--0.5 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1843 0 16 107 1966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221901
X-RAY DIFFRACTIONr_bond_other_d0.0120.021713
X-RAY DIFFRACTIONr_angle_refined_deg1.2941.9582569
X-RAY DIFFRACTIONr_angle_other_deg3.38733984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2035241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.12624.72591
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.85615327
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.5421510
X-RAY DIFFRACTIONr_chiral_restr0.0680.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022143
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02391
X-RAY DIFFRACTIONr_mcbond_it0.731.51190
X-RAY DIFFRACTIONr_mcbond_other0.1441.5485
X-RAY DIFFRACTIONr_mcangle_it1.3821893
X-RAY DIFFRACTIONr_scbond_it2.0733711
X-RAY DIFFRACTIONr_scangle_it3.5244.5672
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 77 -
Rwork0.225 1212 -
all-1289 -
obs--100 %
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)
11.18660.5408-0.25861.9938-1.01291.35730.0099-0.00240.05910.08490.08260.0556-0.035-0.0241-0.09240.08740.01180.00090.11180.01260.090518.8483.02776.418
20.9643-0.36731.28161.5819-0.81291.8464-0.0898-0.07860.02940.05790.13530.189-0.2005-0.195-0.04550.11380.03980.03020.15730.04130.10919.999.67966.735
319.27610.4489-0.309413.37535.74014.8205-0.23350.97070.177-0.1357-0.07080.72640.412-0.56880.30420.5956-0.1463-0.25910.16920.04480.238210.11-0.19962.513
41.5543-0.44150.70321.5239-1.21213.0368-0.0092-0.11250.04460.0882-0.0286-0.0954-0.03630.17910.03790.1366-0.01340.01690.10280.00880.099222.1-7.34584.258
52.6211.74710.42315.82510.43542.4411-0.0450.1128-0.0641-0.05430.06420.04880.0322-0.0715-0.01910.1221-0.0112-0.00060.13560.00190.088120.06-17.60996.195
64.91882.2984-1.059211.52943.3251.62520.0251-0.0820.10650.1872-0.26280.77210.046-0.08060.23770.19510.0632-0.01530.23390.06190.13379.008-20.3992.61
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 75
2X-RAY DIFFRACTION2A76 - 108
3X-RAY DIFFRACTION3A109 - 114
4X-RAY DIFFRACTION4B3 - 92
5X-RAY DIFFRACTION5B93 - 111
6X-RAY DIFFRACTION6B112 - 122

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