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- PDB-3b33: Crystal structure of the PAS domain of nitrogen regulation protei... -

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Basic information

Entry
Database: PDB / ID: 3b33
TitleCrystal structure of the PAS domain of nitrogen regulation protein NR(II) from Vibrio parahaemolyticus
ComponentsSensor protein
KeywordsTRANSFERASE / structural genomics / PAS domain / nitrogen regulation protein / APC91440.4 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / Kinase / Phosphorylation
Function / homology
Function and homology information


histidine kinase / phosphorelay sensor kinase activity / nucleotide binding / regulation of DNA-templated transcription
Similarity search - Function
His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / PAS fold ...His Kinase A (phospho-acceptor) domain / His Kinase A (phosphoacceptor) domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain / PAS domain / Signal transduction histidine kinase, dimerisation/phosphoacceptor domain superfamily / Signal transduction histidine kinase-related protein, C-terminal / Histidine kinase domain / Histidine kinase domain profile. / Beta-Lactamase / PAS fold / PAS fold / PAS domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / PAS domain / PAS domain superfamily / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesVibrio parahaemolyticus RIMD 2210633 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.83 Å
AuthorsOsipiuk, J. / Sather, A. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray structure of PAS domain of nitrogen regulation protein NR(II) from Vibrio parahaemolyticus.
Authors: Osipiuk, J. / Sather, A. / Abdullah, J. / Joachimiak, A.
History
DepositionOct 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sensor protein


Theoretical massNumber of molelcules
Total (without water)12,8511
Polymers12,8511
Non-polymers00
Water1,24369
1
A: Sensor protein

A: Sensor protein


Theoretical massNumber of molelcules
Total (without water)25,7022
Polymers25,7022
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.115, 81.115, 67.467
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-115-

HOH

DetailsAuthors state that the biological unit of this protein is unknown.

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Components

#1: Protein Sensor protein


Mass: 12850.979 Da / Num. of mol.: 1 / Fragment: PAS domain: Residues 1-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus RIMD 2210633 (bacteria)
Species: Vibrio parahaemolyticus / Strain: RIMD 2210633 / Serotype O3:K6 / Gene: VP0119 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q87TF0, histidine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / 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: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M Sodium acetate, 3 M Sodium chloride, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 5, 2007
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.83→35.12 Å / Num. all: 11960 / Num. obs: 11960 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.3 % / Biso Wilson estimate: 40.5 Å2 / Rmerge(I) obs: 0.072 / Χ2: 1.558 / Net I/σ(I): 11.3
Reflection shellResolution: 1.83→1.88 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.18 / Num. unique all: 872 / Χ2: 0.787 / % possible all: 88.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
SBC-Collectdata collection
HKL-3000data reduction
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementResolution: 1.83→35.12 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.969 / SU B: 5.83 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.124 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1958 566 4.7 %RANDOM
Rwork0.1837 ---
all0.1843 11938 --
obs0.1843 11938 98.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.354 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.83→35.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms838 0 0 69 907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022936
X-RAY DIFFRACTIONr_angle_refined_deg1.782.0031300
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4965135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.23125.27836
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.21615182
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.435156
X-RAY DIFFRACTIONr_chiral_restr0.1360.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02680
X-RAY DIFFRACTIONr_nbd_refined0.2240.2421
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2663
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.290.262
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.28
X-RAY DIFFRACTIONr_mcbond_it1.1941.5608
X-RAY DIFFRACTIONr_mcangle_it1.9742985
X-RAY DIFFRACTIONr_scbond_it2.2793357
X-RAY DIFFRACTIONr_scangle_it3.4494.5300
LS refinement shellResolution: 1.83→1.88 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 40 -
Rwork0.269 727 -
all-767 -
obs-767 87.66 %
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)
10.3286-0.52890.52470.9307-0.50382.3028-0.03160.06150.02920.0527-0.0063-0.0885-0.1610.00320.03790.06440.0095-0.09030.08240.00820.048217.065229.66846.6962
29.7219-6.7434-0.912930.951-9.401614.4818-0.0153-0.6625-0.24761.19030.52710.9285-1.031-0.065-0.51180.01980.00380.07270.0576-0.0443-0.12938.337827.68912.9183
327.9516-14.955110.552910.65860.544518.4075-0.834-1.48930.1680.38760.619-0.1747-1.2053-1.48540.2150.07180.0755-0.00790.0473-0.0442-0.080414.965830.803519.1129
42.1052-2.84330.8253.8488-0.823510.0338-0.1273-0.4913-0.20930.06550.37370.0525-0.0964-0.4429-0.2464-0.0918-0.0264-0.06330.08590.1852-0.02815.981415.79918.0837
546.69727.8922-18.994811.35261.205216.97880.474-0.9681-1.0721-0.10210.1248-0.74420.91880.5521-0.5987-0.09950.076-0.0854-0.04580.0740.034827.966613.88587.1582
631.232211.9619-9.36669.55770.38356.31060.07950.3022-1.3278-0.5708-0.10570.05640.9136-0.25180.02620.0744-0.0492-0.1822-0.06670.07420.069916.545711.3494.6686
79.3915-2.5825-10.939616.69835.225726.04810.3953-0.394-0.58560.46150.43661.2115-1.1203-1.843-0.8319-0.12280.052-0.04530.34310.3663-0.02647.477416.939117.2552
819.47581.54430.23931.6609-2.13493.01850.1121-0.39211.47470.0069-0.19940.08560.13180.34630.0873-0.0095-0.0531-0.07010.09380.0220.159424.303623.1136.1325
99.37851.60235.10711.79290.61272.8255-0.0682-0.1676-0.10520.0160.1073-0.10930.0012-0.0859-0.03910.0397-0.0232-0.06880.06590.04130.020516.98420.8696.4927
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 336 - 36
2X-RAY DIFFRACTION2AA34 - 3837 - 41
3X-RAY DIFFRACTION3AA39 - 4842 - 51
4X-RAY DIFFRACTION4AA49 - 6152 - 64
5X-RAY DIFFRACTION5AA62 - 7165 - 74
6X-RAY DIFFRACTION6AA72 - 7775 - 80
7X-RAY DIFFRACTION7AA78 - 8781 - 90
8X-RAY DIFFRACTION8AA88 - 10191 - 104
9X-RAY DIFFRACTION9AA102 - 111105 - 114

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