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- PDB-5z4z: Crystal structure of PaCysB NTD domain with space group C2 -

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Basic information

Entry
Database: PDB / ID: 5z4z
TitleCrystal structure of PaCysB NTD domain with space group C2
ComponentsTranscriptional regulator CysB
KeywordsDNA BINDING PROTEIN / CysB
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.053 Å
AuthorsYang, C. / Liang, H. / Gan, J.
CitationJournal: Mol.Microbiol. / Year: 2019
Title: Molecular insights into the master regulator CysB-mediated bacterial virulence in Pseudomonas aeruginosa.
Authors: Song, Y. / Yang, C. / Chen, G. / Zhang, Y. / Seng, Z. / Cai, Z. / Zhang, C. / Yang, L. / Gan, J. / Liang, H.
History
DepositionJan 15, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator CysB
B: Transcriptional regulator CysB
C: Transcriptional regulator CysB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0344
Polymers30,9383
Non-polymers961
Water2,630146
1
A: Transcriptional regulator CysB
B: Transcriptional regulator CysB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7213
Polymers20,6252
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-37 kcal/mol
Surface area9550 Å2
MethodPISA
2
C: Transcriptional regulator CysB

C: Transcriptional regulator CysB


Theoretical massNumber of molelcules
Total (without water)20,6252
Polymers20,6252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area2160 Å2
ΔGint-24 kcal/mol
Surface area9870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.084, 53.222, 57.456
Angle α, β, γ (deg.)90.00, 91.66, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11C-137-

HOH

21C-143-

HOH

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Components

#1: Protein Transcriptional regulator CysB / CysB / CysB family transcriptional regulator / HTH-type transcriptional regulator CysB / LysR ...CysB / CysB family transcriptional regulator / HTH-type transcriptional regulator CysB / LysR family transcriptional regulator / Transcriptional regulator CysB


Mass: 10312.711 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Plasmid: pET28SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2C6M5K9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.65 Å3/Da / Density % sol: 53.65 %
Description: the entry contains friedel pairs in F-plus/minus columns
Crystal growTemperature: 291.5 K / Method: vapor diffusion, hanging drop
Details: 10% 2-propanol,0.1M sodium phosphate/citric acid PH4.2 0.2M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9725 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9725 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 18944 / % possible obs: 94.2 % / Redundancy: 4.1 % / Rsym value: 0.118 / Net I/σ(I): 13.5
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.376 / Rsym value: 0.309 / % possible all: 88

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IXC

1ixc


Resolution: 2.053→29.444 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.42 / Phase error: 25.51
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 967 5.11 %RANDOM
Rwork0.1954 ---
obs0.1979 18940 93.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.053→29.444 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 5 146 2197
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072078
X-RAY DIFFRACTIONf_angle_d0.8072811
X-RAY DIFFRACTIONf_dihedral_angle_d22.6181253
X-RAY DIFFRACTIONf_chiral_restr0.054336
X-RAY DIFFRACTIONf_plane_restr0.006355
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0531-2.16130.29281450.2312296X-RAY DIFFRACTION86
2.1613-2.29670.42791250.27492312X-RAY DIFFRACTION84
2.2967-2.47390.26111300.22142612X-RAY DIFFRACTION95
2.4739-2.72270.28111290.2082631X-RAY DIFFRACTION97
2.7227-3.11630.24741470.19572691X-RAY DIFFRACTION98
3.1163-3.92480.21661270.1712665X-RAY DIFFRACTION97
3.9248-29.44740.19461640.17672766X-RAY DIFFRACTION99
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)
12.15560.33251.14591.87490.24352.83870.0947-0.1931-0.11030.2868-0.0322-0.16070.3277-0.1531-0.03730.2358-0.06230.04210.1974-0.01870.252729.7597-0.305317.2058
21.7370.61231.33051.12240.89793.9443-0.01160.05990.1028-0.0926-0.009-0.0733-0.11980.16410.01140.1597-0.01060.0470.11680.0240.283727.8465.4844-2.5394
32.2694-0.151.05081.00340.05372.50120.37080.3276-0.239-0.0435-0.1198-0.13980.20380.1103-0.17490.19390.0625-0.03040.1977-0.02040.304250.85916.922517.7844
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:89)
2X-RAY DIFFRACTION2(chain B and resseq 1:90)
3X-RAY DIFFRACTION3(chain C and resseq 1:88)

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