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- PDB-2vut: Crystal structure of NAD-bound NmrA-AreA zinc finger complex -

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Basic information

Entry
Database: PDB / ID: 2vut
TitleCrystal structure of NAD-bound NmrA-AreA zinc finger complex
Components
  • NITROGEN METABOLITE REPRESSION REGULATOR NMRA
  • NITROGEN REGULATORY PROTEIN AREA
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / PROTEIN-PROTEIN INTERACTIONS / METAL-BINDING / NITRATE ASSIMILATION / ZINC-FINGER / DNA-BINDING / ZINC FINGERS / ZINC / AREA / NMRA / NUCLEUS / ACTIVATOR / GATA-TYPE
Function / homology
Function and homology information


nitrogen catabolite repression of transcription from RNA polymerase II promoter / regulation of amide catabolic process / nitrogen catabolite repression of transcription / regulation of arginine metabolic process / regulation of nitrogen utilization / NADP+ binding / NAD+ binding / nitrate assimilation / NAD binding / regulation of gene expression ...nitrogen catabolite repression of transcription from RNA polymerase II promoter / regulation of amide catabolic process / nitrogen catabolite repression of transcription / regulation of arginine metabolic process / regulation of nitrogen utilization / NADP+ binding / NAD+ binding / nitrate assimilation / NAD binding / regulation of gene expression / sequence-specific DNA binding / oxidoreductase activity / DNA-binding transcription factor activity, RNA polymerase II-specific / chromatin remodeling / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus / cytoplasm
Similarity search - Function
Nitrogen regulatory AreA, N-terminal / Nitrogen regulatory protein AreA N terminus / Nitrogen regulatory protein areA, GATA-like domain / Fungal protein of unknown function (DUF1752) / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type ...Nitrogen regulatory AreA, N-terminal / Nitrogen regulatory protein AreA N terminus / Nitrogen regulatory protein areA, GATA-like domain / Fungal protein of unknown function (DUF1752) / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / NmrA-like domain / NmrA-like family / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / Zinc finger, NHR/GATA-type / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nitrogen metabolite repression protein nmrA / Nitrogen regulatory protein areA / Nitrogen metabolite repression protein nmrA
Similarity search - Component
Biological speciesEmericella nidulans (mold)
EMERICELLA NIDULANS (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKotaka, M. / Johnson, C. / Lamb, H.K. / Hawkins, A.R. / Ren, J. / Stammers, D.K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural Analysis of the Recognition of the Negative Regulator Nmra and DNA by the Zinc Finger from the Gata-Type Transcription Factor Area.
Authors: Kotaka, M. / Johnson, C. / Lamb, H.K. / Hawkins, A.R. / Ren, J. / Stammers, D.K.
History
DepositionMay 30, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.4May 8, 2024Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
B: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
C: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
D: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
E: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
F: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
G: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
H: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
I: NITROGEN REGULATORY PROTEIN AREA
J: NITROGEN REGULATORY PROTEIN AREA
K: NITROGEN REGULATORY PROTEIN AREA
L: NITROGEN REGULATORY PROTEIN AREA
M: NITROGEN REGULATORY PROTEIN AREA
N: NITROGEN REGULATORY PROTEIN AREA
O: NITROGEN REGULATORY PROTEIN AREA
P: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)355,35442
Polymers348,99916
Non-polymers6,35526
Water35,2551957
1
A: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
I: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3895
Polymers43,6252
Non-polymers7643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1770 Å2
ΔGint-10.2 kcal/mol
Surface area18300 Å2
MethodPQS
2
B: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
J: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3544
Polymers43,6252
Non-polymers7292
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-8.5 kcal/mol
Surface area18550 Å2
MethodPQS
3
C: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
K: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4816
Polymers43,6252
Non-polymers8564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-8.7 kcal/mol
Surface area18040 Å2
MethodPQS
4
D: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
L: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3895
Polymers43,6252
Non-polymers7643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-9.8 kcal/mol
Surface area18300 Å2
MethodPQS
5
E: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
M: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4816
Polymers43,6252
Non-polymers8564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1850 Å2
ΔGint-8.9 kcal/mol
Surface area18050 Å2
MethodPQS
6
F: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
N: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3895
Polymers43,6252
Non-polymers7643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-6.9 kcal/mol
Surface area17980 Å2
MethodPQS
7
G: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
O: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,4816
Polymers43,6252
Non-polymers8564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-7.3 kcal/mol
Surface area18290 Å2
MethodPQS
8
H: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
P: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3895
Polymers43,6252
Non-polymers7643
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-8.9 kcal/mol
Surface area18230 Å2
MethodPQS
9
A: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5343
Polymers38,8351
Non-polymers6992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
B: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4992
Polymers38,8351
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
C: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6264
Polymers38,8351
Non-polymers7913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
D: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5343
Polymers38,8351
Non-polymers6992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
13
E: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5343
Polymers38,8351
Non-polymers6992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
14
F: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5343
Polymers38,8351
Non-polymers6992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
15
G: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6264
Polymers38,8351
Non-polymers7913
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
16
H: NITROGEN METABOLITE REPRESSION REGULATOR NMRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5343
Polymers38,8351
Non-polymers6992
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
17
I: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,7901
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
18
J: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,7901
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
19
K: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,7901
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
20
L: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,7901
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
21
M: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,9473
Polymers4,7901
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
22
N: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,7901
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
23
O: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,7901
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
24
P: NITROGEN REGULATORY PROTEIN AREA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,8552
Polymers4,7901
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)227.520, 227.520, 222.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11B-2023-

HOH

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Components

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Protein / Protein/peptide , 2 types, 16 molecules ABCDEFGHIJKLMNOP

#1: Protein
NITROGEN METABOLITE REPRESSION REGULATOR NMRA / NMRA


Mass: 38835.238 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold)
Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O59919, UniProt: Q5AU62*PLUS
#2: Protein/peptide
NITROGEN REGULATORY PROTEIN AREA / AREA


Mass: 4789.604 Da / Num. of mol.: 8 / Fragment: ZINC FINGER DOMAIN, RESIDUES 670-712
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) EMERICELLA NIDULANS (mold) / Plasmid: PET3A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P17429

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Non-polymers , 5 types, 1983 molecules

#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1957 / 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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 6.4
Details: 0.2M LI2SO4, 0.1M BIS-TRIS PH 6.4, 15% - 17% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 180785 / % possible obs: 94.8 % / Observed criterion σ(I): -1 / Redundancy: 6 % / Biso Wilson estimate: 22.6 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 12.7
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.6 / % possible all: 71.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1K6J AND 4GAT

1k6j

4gat


Resolution: 2.3→29.86 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 2465599.64 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: A SELF PATTERSON FUNCTION SHOWED A SIGNIFICANT PEAK INDICATIVE OF PSEUDO-TRANSLATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 17971 9.9 %RANDOM
Rwork0.215 ---
obs0.215 180780 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.8585 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 35.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å20 Å20 Å2
2--3.2 Å20 Å2
3----6.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.3→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms22892 0 385 1957 25234
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it5.44
X-RAY DIFFRACTIONc_mcangle_it7.418
X-RAY DIFFRACTIONc_scbond_it9.678
X-RAY DIFFRACTIONc_scangle_it10.9810
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 2467 10 %
Rwork0.293 22290 -
obs--77.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2NAD.PARNAD.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4GOL.PARGOL.TOP
X-RAY DIFFRACTION5ION.PARAM

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