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- PDB-2p6s: Crystal Structure of Transcriptional Regulator NMB0573/L-Met Comp... -

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Basic information

Entry
Database: PDB / ID: 2p6s
TitleCrystal Structure of Transcriptional Regulator NMB0573/L-Met Complex from Neisseria Meningitidis
ComponentsTranscriptional regulator, LRP/AsnC familyTranscriptional regulation
KeywordsTRANSCRIPTION / NMB0573 / Transcriptional regulator / Lrp/AsnC-family / 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
METHIONINE / Transcriptional regulator, AsnC family
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 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: Advisory / 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)148,96937
Polymers146,3108
Non-polymers2,66029
Water3,909217
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39190 Å2
ΔGint-266 kcal/mol
Surface area52030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.831, 149.676, 77.671
Angle α, β, γ (deg.)90.00, 106.01, 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

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11THRTHRLEULEU5AA5 - 1587 - 160
21THRTHRLEULEU5BB5 - 1587 - 160
31THRTHRLEULEU5CC5 - 1587 - 160
41THRTHRLEULEU5DD5 - 1587 - 160
51THRTHRLEULEU5EE5 - 1587 - 160
61THRTHRLEULEU5FF5 - 1587 - 160
71THRTHRLEULEU5GG5 - 1587 - 160
81THRTHRLEULEU5HH5 - 1587 - 160
12METMETMETMET4AI1160
22METMETMETMET4BS1160
32METMETMETMET4CU1160
42METMETMETMET4DY1160
52METMETMETMET4EBA1160
62METMETMETMET4FFA1160
72METMETMETMET4GIA1160
82METMETMETMET4HJA1160

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-MET / METHIONINE / Methionine


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
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: 2.8→30 Å / Num. obs: 35471 / % possible obs: 99.9 % / Observed criterion σ(I): -1.5 / Redundancy: 11.5 % / Rmerge(I) obs: 0.183 / Net I/σ(I): 14.6
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 1.8 / Num. unique all: 3499 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2p5v
Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.873 / SU B: 50.446 / SU ML: 0.473 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.483 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30578 1751 5 %RANDOM
Rwork0.22762 ---
obs0.23164 33226 99.91 %-
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: 59.889 Å2
Baniso -1Baniso -2Baniso -3
1-5.84 Å20 Å211.07 Å2
2---3.9 Å20 Å2
3---4.17 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9844 0 153 217 10214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02210145
X-RAY DIFFRACTIONr_bond_other_d0.0010.026892
X-RAY DIFFRACTIONr_angle_refined_deg0.9961.9813709
X-RAY DIFFRACTIONr_angle_other_deg0.803316853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.22551236
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.83123.996453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.43151831
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2461572
X-RAY DIFFRACTIONr_chiral_restr0.0560.21625
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0211025
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021987
X-RAY DIFFRACTIONr_nbd_refined0.1930.22418
X-RAY DIFFRACTIONr_nbd_other0.180.27349
X-RAY DIFFRACTIONr_nbtor_refined0.1720.24751
X-RAY DIFFRACTIONr_nbtor_other0.0820.25591
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2298
X-RAY DIFFRACTIONr_metal_ion_refined0.1580.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1870.231
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.284
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.170.213
X-RAY DIFFRACTIONr_mcbond_it3.24746545
X-RAY DIFFRACTIONr_mcbond_other0.81942487
X-RAY DIFFRACTIONr_mcangle_it5.106610107
X-RAY DIFFRACTIONr_scbond_it5.42764086
X-RAY DIFFRACTIONr_scangle_it8.057103602
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A913medium positional0.460.5
12B913medium positional0.270.5
13C913medium positional0.320.5
14D913medium positional0.530.5
15E913medium positional0.330.5
16F913medium positional0.280.5
17G913medium positional0.360.5
18H913medium positional0.410.5
21A14medium positional0.110.5
22B14medium positional0.10.5
23C14medium positional0.080.5
24D14medium positional0.070.5
25E14medium positional0.120.5
26F14medium positional0.110.5
27G14medium positional0.380.5
28H14medium positional0.110.5
11A1145loose positional1.155
12B1145loose positional0.995
13C1145loose positional1.045
14D1145loose positional1.195
15E1145loose positional1.155
16F1145loose positional1.025
17G1145loose positional1.125
18H1145loose positional1.095
11A913medium thermal9.3520
12B913medium thermal6.0720
13C913medium thermal5.3120
14D913medium thermal6.0920
15E913medium thermal5.1620
16F913medium thermal6.3420
17G913medium thermal5.8420
18H913medium thermal4.5820
21A14medium thermal2.6620
22B14medium thermal1.4620
23C14medium thermal1.9920
24D14medium thermal2.3120
25E14medium thermal4.2620
26F14medium thermal2.7820
27G14medium thermal4.6520
28H14medium thermal3.0420
11A1145loose thermal13.2230
12B1145loose thermal7.9930
13C1145loose thermal6.5130
14D1145loose thermal7.4530
15E1145loose thermal6.6230
16F1145loose thermal7.3530
17G1145loose thermal7.4230
18H1145loose thermal5.6830
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.523 129 -
Rwork0.438 2426 -
obs--99.49 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.7822-1.50890.07411.39590.26480.9093-0.3861-0.23110.10260.16380.068-0.2786-0.0725-0.04280.3181-0.34230.034-0.091-0.31740.0274-0.31218.4617.876686.9235
21.5020.5438-0.91482.1385-0.33911.7049-0.0680.11520.1699-0.07210.14310.0205-0.021-0.1201-0.0751-0.4351-0.0058-0.0958-0.32910.0249-0.311715.67948.134157.7026
31.83910.2683-0.63730.5328-0.38391.5207-0.00840.016-0.0672-0.00290.027-0.02510.0823-0.1962-0.0186-0.4224-0.0316-0.0104-0.4161-0.0038-0.3144-0.85692.329375.9017
40.5171-0.4679-0.77882.93790.40651.20820.062-0.2233-0.0461-0.09930.0375-0.05430.12120.0819-0.0995-0.40460.0258-0.0506-0.3014-0.0219-0.279529.621311.604873.9308
51.99241.9295-0.81512.8033-0.26321.20220.0020.07980.1606-0.0207-0.119-0.0320.1165-0.29440.117-0.4191-0.0530.0007-0.43980.0296-0.285322.0036-31.394751.9771
61.4496-0.139-1.1321.3840.04350.8871-0.06810.22390.0062-0.12970.03350.2016-0.0135-0.10010.0346-0.3695-0.0035-0.0524-0.2635-0.0063-0.330330.5592-3.715538.7209
73.32891.0002-2.663.1236-1.12952.9334-0.75950.7773-0.7954-0.63160.233-0.20340.628-0.4530.5265-0.2823-0.1480.1549-0.2605-0.1869-0.108430.993-27.93732.6944
82.89360.6596-0.09620.78570.361.1562-0.0717-0.0905-0.05310.1894-0.0086-0.05070.05220.03360.0803-0.40.0059-0.0182-0.41180.034-0.302833.8438-10.361159.1453
91.6956-0.3339-1.64270.09580.53053.01570.0308-0.1415-0.0552-0.0572-0.05580.04510.32830.04110.025-0.284-0.02810.0335-0.39660.0133-0.318668.6378-0.560325.8345
101.62510.8271-0.17730.880.22391.7827-0.08080.0775-0.0497-0.1030.08430.0519-0.1133-0.227-0.0035-0.4030.00090.0026-0.33930.0281-0.32845.644218.391436.7057
111.99230.8567-0.41860.4272-0.27971.3265-0.05520.01660.137-0.1638-0.0608-0.025-0.0274-0.05280.116-0.36120.00280.0404-0.39290.0187-0.29667.711920.478824.8304
120.37910.63540.05991.13110.37531.15460.0122-0.0623-0.0592-0.1650.0473-0.1629-0.0242-0.0648-0.0595-0.41370.00180.0317-0.3913-0.0059-0.293854.64351.55846.8993
130.91270.57950.07871.6739-0.69691.7395-0.2735-0.05810.2268-0.16710.1348-0.2938-0.06560.32020.1387-0.4074-0.04320.0524-0.355-0.0006-0.128656.323648.460661.4659
1410.4674-0.00082.010.35811.6443-0.00480.10250.0744-0.14150.09070.2513-0.0974-0.1564-0.0859-0.42830.0281-0.0268-0.35910.0122-0.243730.75430.260555.7071
151.2173-1.2594-1.32882.82490.91471.5895-0.0263-0.12480.14630.09930.172-0.15850.00030.0925-0.1457-0.34960.00650.0259-0.4445-0.0232-0.255835.711851.579767.9102
161.60380.5359-1.17791.7753-0.13411.36420.18740.00940.06720.13240.0095-0.0905-0.02840.0951-0.1969-0.45860.0069-0.0622-0.34920.0143-0.284550.476423.729761.7987
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 605 - 62
2X-RAY DIFFRACTION1AA146 - 158148 - 160
3X-RAY DIFFRACTION2AA61 - 14563 - 147
4X-RAY DIFFRACTION3BB3 - 605 - 62
5X-RAY DIFFRACTION3BB146 - 158148 - 160
6X-RAY DIFFRACTION4BB61 - 14563 - 147
7X-RAY DIFFRACTION5CC5 - 607 - 62
8X-RAY DIFFRACTION5CC146 - 158148 - 160
9X-RAY DIFFRACTION6CC61 - 14563 - 147
10X-RAY DIFFRACTION7DD3 - 605 - 62
11X-RAY DIFFRACTION7DD146 - 158148 - 160
12X-RAY DIFFRACTION8DD61 - 14563 - 147
13X-RAY DIFFRACTION9EE3 - 605 - 62
14X-RAY DIFFRACTION9EE146 - 158148 - 160
15X-RAY DIFFRACTION10EE61 - 14563 - 147
16X-RAY DIFFRACTION11FF5 - 607 - 62
17X-RAY DIFFRACTION11FF146 - 158148 - 160
18X-RAY DIFFRACTION12FF61 - 14563 - 147
19X-RAY DIFFRACTION13GG1 - 603 - 62
20X-RAY DIFFRACTION13GG146 - 158148 - 160
21X-RAY DIFFRACTION14GG61 - 14563 - 147
22X-RAY DIFFRACTION15HH5 - 607 - 62
23X-RAY DIFFRACTION15HH146 - 158148 - 160
24X-RAY DIFFRACTION16HH61 - 14563 - 147

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