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- PDB-2p6t: CRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR NMB0573 and L-LEUC... -

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Basic information

Entry
Database: PDB / ID: 2p6t
TitleCRYSTAL STRUCTURE OF TRANSCRIPTIONAL REGULATOR NMB0573 and L-LEUCINE COMPLEX FROM NEISSERIA MENINGITIDIS
ComponentsTranscriptional regulator, LRP/AsnC familyTranscriptional regulation
KeywordsTRANSCRIPTION / NMB0573 / Transcriptional regulator / Lrp/AsnC-family / N. Meninigitidis / Structural Genomics / Structural and functional analysis of N. meninigitidis transcriptional regulators / Oxford Protein Production Facility / OPPF
Function / homology
Function and homology information


response to amino acid / sequence-specific DNA binding / metal ion binding / cytosol
Similarity search - Function
Transcription regulator HTH, AsnC-type, conserved site / AsnC-type HTH domain signature. / AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / AsnC-type HTH domain / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Winged helix-turn-helix DNA-binding ...Transcription regulator HTH, AsnC-type, conserved site / AsnC-type HTH domain signature. / AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / AsnC-type HTH domain / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Winged helix-turn-helix DNA-binding / ArsR-like helix-turn-helix domain / Dimeric alpha-beta barrel / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
LEUCINE / Transcriptional regulator, AsnC family
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsRen, J. / Sainsbury, S. / Owens, R.J. / Oxford Protein Production Facility (OPPF)
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The Structure and Transcriptional Analysis of a Global Regulator from Neisseria meningitidis.
Authors: Ren, J. / Sainsbury, S. / Combs, S.E. / Capper, R.G. / Jordan, P.W. / Berrow, N.S. / Stammers, D.K. / Saunders, N.J. / Owens, R.J.
History
DepositionMar 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, LRP/AsnC family
B: Transcriptional regulator, LRP/AsnC family
C: Transcriptional regulator, LRP/AsnC family
D: Transcriptional regulator, LRP/AsnC family
E: Transcriptional regulator, LRP/AsnC family
F: Transcriptional regulator, LRP/AsnC family
G: Transcriptional regulator, LRP/AsnC family
H: Transcriptional regulator, LRP/AsnC family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,35233
Polymers146,3108
Non-polymers2,04325
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37810 Å2
ΔGint-306 kcal/mol
Surface area52620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.389, 149.771, 77.845
Angle α, β, γ (deg.)90.00, 105.68, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
12A
22B
32C
42D
52E
62F
72G
82H

NCS domain segments:

Component-ID: 1 / End auth comp-ID: LEU / End label comp-ID: LEU

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHR5AA5 - 1587 - 160
21THRTHR5BB5 - 1587 - 160
31THRTHR5CC5 - 1587 - 160
41THRTHR5DD5 - 1587 - 160
51THRTHR5EE5 - 1587 - 160
61THRTHR5FF5 - 1587 - 160
71THRTHR5GG5 - 1587 - 160
81THRTHR5HH5 - 1587 - 160
12LEULEU4AI1160
22LEULEU4BM1160
32LEULEU4CP1160
42LEULEU4DS1160
52LEULEU4EX1160
62LEULEU4FAA1160
72LEULEU4GCA1160
82LEULEU4HGA1160

NCS ensembles :
ID
1
2

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Components

#1: Protein
Transcriptional regulator, LRP/AsnC family / Transcriptional regulation


Mass: 18288.701 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: NMB0573 / Plasmid: OPPF2146 / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q9K0L9
#2: Chemical
ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.49 Å3/Da / Density % sol: 50.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 95 mM HEPES-Na, 190 mM Calcium Chloride, 26.6% PEG 400, 5% Glycerol, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 9, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 28887 / % possible obs: 91.2 % / Observed criterion σ(I): -1.5 / Redundancy: 2.7 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 6.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 1.3 / Num. unique all: 2007 / % possible all: 63.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2p5v

2p5v


Resolution: 2.9→30 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.872 / SU B: 27.65 / SU ML: 0.483 / Cross valid method: THROUGHOUT / ESU R Free: 0.544 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30008 1454 4.9 %RANDOM
Rwork0.23534 ---
obs0.23853 28166 92.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 48.167 Å2
Baniso -1Baniso -2Baniso -3
1-4.3 Å20 Å211.39 Å2
2---2.29 Å20 Å2
3---4.15 Å2
Refinement stepCycle: LAST / Resolution: 2.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9844 0 119 132 10095
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210115
X-RAY DIFFRACTIONr_bond_other_d0.0020.026852
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.9813686
X-RAY DIFFRACTIONr_angle_other_deg0.798316763
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.82551236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3723.982452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.131151825
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6491572
X-RAY DIFFRACTIONr_chiral_restr0.0570.21633
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211021
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021987
X-RAY DIFFRACTIONr_nbd_refined0.2180.22559
X-RAY DIFFRACTIONr_nbd_other0.1950.27740
X-RAY DIFFRACTIONr_nbtor_refined0.1770.24881
X-RAY DIFFRACTIONr_nbtor_other0.0840.25641
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2321
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0480.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1570.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.235
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.288
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2390.27
X-RAY DIFFRACTIONr_mcbond_it3.57646516
X-RAY DIFFRACTIONr_mcbond_other0.88842487
X-RAY DIFFRACTIONr_mcangle_it5.791610107
X-RAY DIFFRACTIONr_scbond_it6.1564065
X-RAY DIFFRACTIONr_scangle_it9.229103579
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A913medium positional0.440.5
12B913medium positional0.310.5
13C913medium positional0.40.5
14D913medium positional0.60.5
15E913medium positional0.350.5
16F913medium positional0.280.5
17G913medium positional0.430.5
18H913medium positional0.40.5
21A13medium positional0.160.5
22B13medium positional0.090.5
23C13medium positional0.070.5
24D13medium positional0.070.5
25E13medium positional0.20.5
26F13medium positional0.120.5
27G13medium positional0.150.5
28H13medium positional0.060.5
11A1144loose positional1.195
12B1144loose positional1.085
13C1144loose positional1.035
14D1144loose positional1.275
15E1144loose positional1.125
16F1144loose positional0.935
17G1144loose positional1.075
18H1144loose positional1.095
11A913medium thermal7.0520
12B913medium thermal6.9320
13C913medium thermal6.4720
14D913medium thermal9.7220
15E913medium thermal6.6820
16F913medium thermal8.0620
17G913medium thermal7.6320
18H913medium thermal5.9420
21A13medium thermal2.8920
22B13medium thermal2.4420
23C13medium thermal8.6120
24D13medium thermal3.5920
25E13medium thermal11.2420
26F13medium thermal5.9720
27G13medium thermal4.5120
28H13medium thermal3.8720
11A1144loose thermal7.9330
12B1144loose thermal9.7430
13C1144loose thermal7.5930
14D1144loose thermal10.8630
15E1144loose thermal8.8630
16F1144loose thermal9.830
17G1144loose thermal9.4830
18H1144loose thermal7.9930
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.457 65 -
Rwork0.445 1490 -
obs--65.72 %

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