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- PDB-4ab5: Regulatory domain structure of NMB2055 (MetR) a LysR family regul... -

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Basic information

Entry
Database: PDB / ID: 4ab5
TitleRegulatory domain structure of NMB2055 (MetR) a LysR family regulator from N. meningitidis
ComponentsTRANSCRIPTIONAL REGULATOR, LYSR FAMILY
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTORS
Function / homology
Function and homology information


methionine biosynthetic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / cytoplasm
Similarity search - Function
HTH-type transcriptional regulator MetR, PBP2 domain / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...HTH-type transcriptional regulator MetR, PBP2 domain / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional regulator MetR
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS SEROGROUP B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.51 Å
AuthorsSainsbury, S. / Ren, J. / Saunders, N.J. / Stuart, D.I. / Owens, R.J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: Structure of the Regulatory Domain of the Lysr Family Regulator Nmb2055 (Metr-Like Protein) from Neisseria Meningitidis
Authors: Sainsbury, S. / Ren, J. / Saunders, N.J. / Stuart, D.I. / Owens, R.J.
History
DepositionDec 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATOR, LYSR FAMILY
B: TRANSCRIPTIONAL REGULATOR, LYSR FAMILY


Theoretical massNumber of molelcules
Total (without water)50,3282
Polymers50,3282
Non-polymers00
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-10.4 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.140, 52.570, 65.890
Angle α, β, γ (deg.)90.00, 94.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9969, -0.03232, 0.07188), (-0.03865, -0.5944, -0.8032), (0.06869, -0.8035, 0.5913)
Vector: -28.23, 12.53, 7.642)

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Components

#1: Protein TRANSCRIPTIONAL REGULATOR, LYSR FAMILY / NMB2055 / LYSR FAMILY


Mass: 25163.973 Da / Num. of mol.: 2 / Fragment: REGULATORY DOMAIN, RESIDUES 90-309
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS SEROGROUP B (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q9JXG8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.6 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.979
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 13879 / % possible obs: 90 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 50.49 Å2 / Rmerge(I) obs: 0.1

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Processing

SoftwareName: BUSTER / Version: 2.11.2 / Classification: refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.51→21.58 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.8827 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.312
RfactorNum. reflection% reflectionSelection details
Rfree0.2377 700 5.05 %RANDOM
Rwork0.1861 ---
obs0.1887 13850 89.88 %-
Displacement parametersBiso mean: 44.38 Å2
Baniso -1Baniso -2Baniso -3
1-0.9694 Å20 Å2-1.848 Å2
2--1.5752 Å20 Å2
3----2.5447 Å2
Refine analyzeLuzzati coordinate error obs: 0.353 Å
Refinement stepCycle: LAST / Resolution: 2.51→21.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3446 0 0 182 3628
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093536HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.124817HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1202SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes89HARMONIC2
X-RAY DIFFRACTIONt_gen_planes504HARMONIC5
X-RAY DIFFRACTIONt_it3536HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.55
X-RAY DIFFRACTIONt_other_torsion19.39
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion465SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4058SEMIHARMONIC4
LS refinement shellResolution: 2.51→2.71 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.28 111 5.68 %
Rwork0.2081 1844 -
all0.2122 1955 -
obs--89.88 %
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)
10.6391-0.0099-0.1174.43621.07591.03690.0589-0.0326-0.02170.6071-0.0432-0.10880.07380.0681-0.01570.0294-0.0204-0.0653-0.02270.0342-0.2065-0.0548-0.995416.4798
20.9281-0.0689-0.35862.11510.76310.48890.02870.0410.05360.33380.00090.7355-0.01730.0106-0.02960.07470.00010.1881-0.0253-0.0050.1879-26.95490.576918.2389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESSEQ 92:307
2X-RAY DIFFRACTION2CHAIN B AND RESSEQ 89:308

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