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- PDB-5aip: Crystal structure of NadR in complex with 4-hydroxyphenylacetate -

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Basic information

Entry
Database: PDB / ID: 5aip
TitleCrystal structure of NadR in complex with 4-hydroxyphenylacetate
ComponentsTRANSCRIPTIONAL REGULATOR, MARR FAMILY
KeywordsTRANSCRIPTION / CELL ADHESION / VACCINE / MENINGITIS
Function / homology
Function and homology information


DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
HTH-type transcriptional regulator HpaR/FarR / Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...HTH-type transcriptional regulator HpaR/FarR / Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / : / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
4-HYDROXYPHENYLACETATE / Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS SEROGROUP B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsLiguori, A. / Malito, E. / Bottomley, M.J.
CitationJournal: Plos Pathog. / Year: 2016
Title: Molecular Basis of Ligand-Dependent Regulation of Nadr, the Transcriptional Repressor of Meningococcal Virulence Factor Nada.
Authors: Liguori, A. / Malito, E. / Lo Surdo, P. / Fagnocchi, L. / Cantini, F. / Haag, A.F. / Brier, S. / Pizza, M. / Delany, I. / Bottomley, M.J.
History
DepositionFeb 16, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1May 11, 2016Group: Database references
Revision 1.2Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.3Jan 10, 2024Group: 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 / struct_conn / struct_site
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_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSCRIPTIONAL REGULATOR, MARR FAMILY
B: TRANSCRIPTIONAL REGULATOR, MARR FAMILY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6403
Polymers33,4882
Non-polymers1521
Water81145
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5520 Å2
ΔGint-34.4 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.310, 75.310, 91.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-2012-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9275, 0.3691, 0.0601), (0.3598, 0.8372, 0.4118), (0.1017, 0.4036, -0.9093)
Vector: 57.1539, -20.5919, 40.8422)

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Components

#1: Protein TRANSCRIPTIONAL REGULATOR, MARR FAMILY / NEISSERIAL ADHESIN A REGULATOR


Mass: 16743.811 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) NEISSERIA MENINGITIDIS SEROGROUP B (bacteria)
Strain: MC58 / Plasmid: PET15B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): T1R / References: UniProt: Q7DD70
#2: Chemical ChemComp-4HP / 4-HYDROXYPHENYLACETATE


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 1.98 Å3/Da / Density % sol: 38 % / Description: MR-SAD
Crystal growpH: 6.5
Details: H4 MORPHEUS SCREEN (MOLECULAR M AMINO ACIDS, PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.3→46 Å / Num. obs: 12320 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 23.6 % / Biso Wilson estimate: 23.88 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 25.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 23.2 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 9 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: 2FBI
Resolution: 2.3→39.197 Å / SU ML: 0.23 / σ(F): 1.96 / Phase error: 23.46 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2602 585 4.8 %
Rwork0.2091 --
obs0.2115 12273 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.8 Å2
Refinement stepCycle: LAST / Resolution: 2.3→39.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 11 45 2238
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082238
X-RAY DIFFRACTIONf_angle_d1.0853014
X-RAY DIFFRACTIONf_dihedral_angle_d12.596880
X-RAY DIFFRACTIONf_chiral_restr0.046356
X-RAY DIFFRACTIONf_plane_restr0.006391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.53150.28851440.22362848X-RAY DIFFRACTION100
2.5315-2.89770.26571560.2262871X-RAY DIFFRACTION100
2.8977-3.65040.29341340.21772897X-RAY DIFFRACTION100
3.6504-39.20280.23171510.19253072X-RAY DIFFRACTION100
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)
11.24390.2954-0.12152.9639-4.90018.83910.1146-0.08670.0578-0.066-0.0841-0.1370.26760.54280.01050.188-0.01360.0090.2445-0.07740.292239.810517.477825.8242
23.1511.243-1.66734.17781.21933.8684-0.10880.3435-0.38570.0832-0.02760.02120.1776-0.24430.04720.1881-0.02580.02560.178-0.05520.286824.00479.046836.8705
33.5865-0.59020.96691.3613-0.85531.7366-0.10621.0292-0.6271-0.1354-0.25320.42930.3446-0.21190.18930.222-0.03430.010.4319-0.07930.385710.56727.778541.5195
43.35070.21650.18551.17870.07551.6695-0.0616-0.3724-0.3940.1012-0.04830.08210.02750.09-0.07470.16020.0219-0.04170.1121-0.01550.138932.992815.381445.5067
57.70052.0712.67288.39760.10058.0792-0.2996-0.6275-0.20060.7881-0.0652-0.0076-0.7226-0.58220.43720.27530.0550.05950.17420.00720.23631.73929.866833.8355
60.3772-0.4344-0.28450.65880.09861.47650.08260.1153-0.1882-0.2096-0.0970.06220.3001-0.21660.00870.1353-0.09290.0039-0.0023-0.13020.171231.723717.121117.5914
73.82841.4203-1.54262.7618-0.16123.8003-0.3273-0.3849-0.1196-0.07950.0387-0.2521-0.06041.29860.18410.1389-0.01620.0050.3983-0.06750.205246.700211.425717.8038
81.8435-0.08960.26822.194-0.45862.92920.4073-0.1198-0.30220.19580.1911-0.32310.64760.40620.62510.17870.0004-0.10570.1237-0.0980.129540.62513.850911.5856
93.32033.6353-2.00547.8284-2.65066.99390.0467-0.2208-0.39090.1612-0.0593-1.36570.24481.612-0.71570.19640.03530.03870.3832-0.18960.251149.54127.70646.4175
104.9804-3.9613-4.21845.27594.37365.7430.21270.63550.4225-0.5698-0.0586-0.1563-0.1513-0.62080.06690.1879-0.1164-0.09780.12180.05440.150631.799925.26129.0913
113.2767-1.13750.93353.3337-1.13082.1087-0.28920.3928-0.22810.5593-0.1168-0.108-0.21550.36710.09580.1953-0.1090.04820.066-0.02240.161640.729.298228.3489
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 1 THROUGH 31 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 32 THROUGH 76 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 77 THROUGH 91 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 92 THROUGH 122 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 123 THROUGH 140 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 9 THROUGH 48 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 49 THROUGH 63 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 64 THROUGH 76 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 77 THROUGH 97 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 98 THROUGH 122 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 123 THROUGH 145 )

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