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- PDB-5aiq: Crystal structure of ligand-free NadR -

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Basic information

Entry
Database: PDB / ID: 5aiq
TitleCrystal structure of ligand-free NadR
ComponentsTRANSCRIPTIONAL REGULATOR, MARR FAMILY
KeywordsTRANSCRIPTION / CELL ADHESION / VACCINE / MENINGITIS
Function / homology
Function and homology information


response to stress / 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
Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesNEISSERIA MENINGITIDIS SEROGROUP B (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.716 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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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
C: TRANSCRIPTIONAL REGULATOR, MARR FAMILY
D: TRANSCRIPTIONAL REGULATOR, MARR FAMILY


Theoretical massNumber of molelcules
Total (without water)66,4134
Polymers66,4134
Non-polymers00
Water34219
1
C: TRANSCRIPTIONAL REGULATOR, MARR FAMILY
D: TRANSCRIPTIONAL REGULATOR, MARR FAMILY


Theoretical massNumber of molelcules
Total (without water)33,2062
Polymers33,2062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-44.2 kcal/mol
Surface area13570 Å2
MethodPISA
2
A: TRANSCRIPTIONAL REGULATOR, MARR FAMILY
B: TRANSCRIPTIONAL REGULATOR, MARR FAMILY


Theoretical massNumber of molelcules
Total (without water)33,2062
Polymers33,2062
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-41.9 kcal/mol
Surface area13420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.470, 69.470, 253.880
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.0921, 0.0552, 0.9942), (0.0801, -0.9956, 0.0478), (0.9925, 0.0752, -0.0961)11.449, 34.5942, -15.2457
2given(-0.0171, 0.0685, 0.9975), (-0.481, 0.874, -0.0683), (-0.8765, -0.481, 0.018)-11.0844, -1.5926, -65.6717
3given(0.9386, -0.3429, -0.0385), (0.338, -0.936, 0.0984), (-0.0698, 0.0793, 0.9944)-56.3618, 27.2969, -24.9603

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Components

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


Mass: 16603.125 Da / Num. of mol.: 4
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / 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: 2.25 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growDetails: 50 % PEG 3350, 0.13 M DI-AMMONIUM HYDROGEN CITRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Aug 13, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→48.2 Å / Num. obs: 17700 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 12.7 % / Biso Wilson estimate: 49.15 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 22.6
Reflection shellResolution: 2.72→2.88 Å / Redundancy: 12.8 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 3.8 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5AIP

5aip


Resolution: 2.716→48.228 Å / SU ML: 0.37 / σ(F): 2.37 / Phase error: 25.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2722 884 5 %
Rwork0.2175 --
obs0.2201 17698 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.3 Å2
Refinement stepCycle: LAST / Resolution: 2.716→48.228 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4144 0 0 19 4163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034173
X-RAY DIFFRACTIONf_angle_d0.8235621
X-RAY DIFFRACTIONf_dihedral_angle_d10.9911615
X-RAY DIFFRACTIONf_chiral_restr0.029680
X-RAY DIFFRACTIONf_plane_restr0.003723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7162-2.88630.3281440.28112748X-RAY DIFFRACTION100
2.8863-3.10910.31571430.2832713X-RAY DIFFRACTION100
3.1091-3.4220.31151440.24272740X-RAY DIFFRACTION100
3.422-3.91690.2811470.21322788X-RAY DIFFRACTION100
3.9169-4.93410.2141480.18082821X-RAY DIFFRACTION100
4.9341-48.23580.26831580.20463004X-RAY DIFFRACTION100
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)
13.6382-0.2855-2.19332.31150.16631.073-0.04520.175-0.12720.24310.17080.12260.1127-0.0897-0.20310.39450.03560.02080.27260.0320.3348-23.882910.6026-24.5755
27.98931.9945-1.13053.7192-0.94960.34580.38681.07782.51580.25620.29851.5238-0.6223-0.2759-0.48390.5170.06140.11880.43660.20320.9193-35.063522.2399-24.2639
32.56471.88050.96363.5894-0.96441.46250.3495-0.525-0.00180.6927-0.17490.2306-0.0523-0.0407-0.13830.55160.03110.14230.3801-0.09320.2597-20.897114.6303-15.7157
41.2566-0.6434-2.86292.54481.70916.3750.12350.01290.2667-0.0662-0.00310.1039-0.02090.0319-0.12080.2643-0.0280.02740.2543-0.02780.2967-13.972220.8346-35.5973
55.82773.2288-1.16242.99751.25986.1026-0.04060.2207-0.1465-0.3938-0.1105-0.41770.8476-0.29840.06660.51010.03340.05590.2128-0.01130.2815-15.37458.4505-44.4193
64.0018-1.2933-0.24525.2078-1.35041.3899-0.6549-0.569-0.23320.22971.465-0.2371.5897-0.4636-0.49190.81710.014-0.10020.49710.1480.2692-10.76888.6781-52.1427
71.40510.8088-1.26814.41913.46495.18710.06420.07230.2168-0.30880.2781-0.2853-0.18310.83-0.2320.40560.06960.0220.34550.03390.3062-4.653923.5558-40.2456
83.07031.608-0.62076.5969-1.3667.2411-0.173-0.4002-0.41160.76390.3525-0.46560.53670.9831-0.18240.35520.02210.02880.3651-0.03890.3342-6.05311.8464-22.4617
93.0917-0.12540.2325.35790.28972.5746-0.2887-0.64330.20870.40220.49070.2193-0.06110.2389-0.02890.31520.00710.05040.5486-0.02470.2946-38.6871-8.2933-4.4493
107.7597-0.15973.26836.7671-0.91819.1688-0.09010.71540.11840.17460.40041.06940.2524-0.6587-0.31960.3522-0.04460.09580.5960.04780.4368-48.2107-4.0522-19.6495
112.4685-0.5766-0.54072.51561.02219.05460.37261.70690.6056-1.24410.04930.8073-0.0048-0.5731-0.85760.5208-0.0250.01520.82980.12460.5163-42.3156-1.33-27.5808
126.76970.2739-4.34783.024-4.33768.50850.98141.73180.1769-1.4190.8855-0.7641.05540.2823-0.89680.4275-0.1571-0.0580.7065-0.36830.5672-49.5243-5.8837-31.6579
134.7619-4.35333.46474.266-4.43488.90740.98241.5344-0.3193-0.584-1.22341.21020.61120.61620.41980.7012-0.204-0.19570.75040.15260.799-53.9691-3.7765-28.5114
143.8242-0.85382.09250.5969-0.20892.34070.0426-0.7260.69220.12-1.00620.1911.2537-1.19740.89370.7074-0.27790.14220.697-0.15770.9211-48.7689-19.356-14.2031
156.5824-4.00511.66799.4205-2.77254.25720.5140.6287-0.4191-0.0059-0.37341.2012-0.3781-0.8592-0.09820.42650.09020.02130.81950.030.2919-53.2534-6.0917-0.285
167.42625.83421.02577.9509-3.16193.78950.47060.87090.81831.60670.0302-0.0486-0.6845-0.4144-0.31630.71420.21120.25410.6350.09460.6041-41.02095.0376-5.4479
178.17471.5549-1.76497.2256.86618.26670.1243-0.22580.211-0.18470.0115-0.0729-0.24110.3227-0.11240.5263-0.0695-0.10710.36880.10150.3406-25.0243-1.0511-0.6935
185.2461-0.1568-2.00221.8574-0.39551.05250.4895-0.26720.82250.6574-0.1738-0.0194-0.43490.009-0.38390.6935-0.1162-0.01530.4876-0.01440.3438-36.08531.15426.6458
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 9 THROUGH 47 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 48 THROUGH 83 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 92 THROUGH 145 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 9 THROUGH 48 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 49 THROUGH 76 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 77 THROUGH 92 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 93 THROUGH 122 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 123 THROUGH 145 )
9X-RAY DIFFRACTION9CHAIN 'C' AND (RESID 5 THROUGH 31 )
10X-RAY DIFFRACTION10CHAIN 'C' AND (RESID 32 THROUGH 63 )
11X-RAY DIFFRACTION11CHAIN 'C' AND (RESID 64 THROUGH 76 )
12X-RAY DIFFRACTION12CHAIN 'C' AND (RESID 77 THROUGH 83 )
13X-RAY DIFFRACTION13CHAIN 'C' AND (RESID 92 THROUGH 97 )
14X-RAY DIFFRACTION14CHAIN 'C' AND (RESID 98 THROUGH 122 )
15X-RAY DIFFRACTION15CHAIN 'C' AND (RESID 123 THROUGH 140 )
16X-RAY DIFFRACTION16CHAIN 'D' AND (RESID 9 THROUGH 32 )
17X-RAY DIFFRACTION17CHAIN 'D' AND (RESID 33 THROUGH 76 )
18X-RAY DIFFRACTION18CHAIN 'D' AND (RESID 77 THROUGH 144 )

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