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- PDB-7rhe: Crystal Structure of ROK family protein from Burkholderia vietnam... -

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Basic information

Entry
Database: PDB / ID: 7rhe
TitleCrystal Structure of ROK family protein from Burkholderia vietnamiensis G4
ComponentsROK family protein
KeywordsTRANSCRIPTION / SSGCID / NagC/XylR / Bcep1808_1509 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyROK family / ROK family / ATPase, nucleotide binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ROK family protein
Function and homology information
Biological speciesBurkholderia vietnamiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of ROK family protein from Burkholderia vietnamiensis G4
Authors: Abendroth, J. / Delker, S.L. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionJul 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ROK family protein


Theoretical massNumber of molelcules
Total (without water)45,0441
Polymers45,0441
Non-polymers00
Water1,36976
1
A: ROK family protein

A: ROK family protein


Theoretical massNumber of molelcules
Total (without water)90,0892
Polymers90,0892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area3230 Å2
ΔGint-27 kcal/mol
Surface area29900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.410, 112.410, 63.090
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z
Components on special symmetry positions
IDModelComponents
11A-571-

HOH

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Components

#1: Protein ROK family protein


Mass: 45044.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria)
Strain: G4 / LMG 22486 / Gene: Bcep1808_1509 / Plasmid: BuviA.12797.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A4JE13
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.56 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: RigakuReagents JCSG+ screen, condition H7: 200mM ammonium sulfate, 100mM BisTris pH 5.5, 25% (w/V) PEG 3350: BuviA.12797.a.B1.PS02541 at 19.5mg/ml + 2mM ADP 4mM glucose + 2mM MgCl2': tray ...Details: RigakuReagents JCSG+ screen, condition H7: 200mM ammonium sulfate, 100mM BisTris pH 5.5, 25% (w/V) PEG 3350: BuviA.12797.a.B1.PS02541 at 19.5mg/ml + 2mM ADP 4mM glucose + 2mM MgCl2': tray 269309 h7: cryio: 20% EG: puck: ocr0-5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 3, 2016 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20667 / % possible obs: 99.6 % / Redundancy: 8.413 % / Biso Wilson estimate: 55.337 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.054 / Rrim(I) all: 0.057 / Χ2: 1.025 / Net I/σ(I): 24.05
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.3-2.368.4970.5783.7915140.9110.616100
2.36-2.428.4610.4884.4214800.9360.519100
2.42-2.498.5770.3855.6114410.9540.40999.9
2.49-2.578.520.3266.5713870.9670.348100
2.57-2.668.5060.2587.9113470.9780.275100
2.66-2.758.4860.19310.6113270.9870.20599.8
2.75-2.858.5080.15213.1712620.9920.162100
2.85-2.978.4960.11316.6812270.9950.1299.9
2.97-3.18.5150.09619.7211630.9960.10299.9
3.1-3.258.4380.07524.6311200.9980.0899.8
3.25-3.438.4770.05731.3710570.9980.0699.6
3.43-3.648.3880.04837.8510190.9990.05299.7
3.64-3.898.3410.04142.829560.9990.04399.6
3.89-4.28.290.03748.48900.9990.03999.4
4.2-4.68.2950.03454.328160.9990.03699.1
4.6-5.148.2290.03256.467570.9990.03499.5
5.14-5.948.2460.0354.756420.9990.03298.5
5.94-7.278.1630.02657.0256610.02898.6
7.27-10.298.0070.0265.0744810.02198.5
10.29-506.9480.01963.782480.9990.02191.5

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.19refinement
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ab-initio model from RobeTTA-fold

Resolution: 2.3→48.67 Å / SU ML: 0.2775 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1446
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2184 10.57 %0
Rwork0.1993 18478 --
obs0.2047 20662 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.6 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2660 0 0 76 2736
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00612710
X-RAY DIFFRACTIONf_angle_d0.81553703
X-RAY DIFFRACTIONf_chiral_restr0.0502438
X-RAY DIFFRACTIONf_plane_restr0.0074492
X-RAY DIFFRACTIONf_dihedral_angle_d13.4251947
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.350.36011460.28541142X-RAY DIFFRACTION100
2.35-2.40.27641390.26251122X-RAY DIFFRACTION100
2.4-2.460.31751400.25281147X-RAY DIFFRACTION99.92
2.46-2.530.28231290.22971164X-RAY DIFFRACTION100
2.53-2.610.27081400.23741125X-RAY DIFFRACTION100
2.61-2.690.28141370.23421157X-RAY DIFFRACTION100
2.69-2.790.29081130.22921152X-RAY DIFFRACTION99.84
2.79-2.90.27841570.23531126X-RAY DIFFRACTION99.84
2.9-3.030.25791210.22651169X-RAY DIFFRACTION99.92
3.03-3.190.30011220.21851178X-RAY DIFFRACTION99.92
3.19-3.390.27881610.22621136X-RAY DIFFRACTION99.85
3.39-3.650.25491420.20011130X-RAY DIFFRACTION99.69
3.65-4.020.2221330.18261180X-RAY DIFFRACTION99.55
4.02-4.60.21290.16241163X-RAY DIFFRACTION99.46
4.6-5.790.23041450.18831166X-RAY DIFFRACTION99.09
5.8-48.670.22371300.16891221X-RAY DIFFRACTION98.04
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)
12.5398633673-0.4298091152750.7470469176470.120123558326-0.01589849731930.5813212817910.1815916670910.09252726904480.926562372197-0.2347227138320.661288363891-0.43704629858-0.3865971706830.198406227632-0.7373773834920.683578325603-0.1538813294040.2493653294650.702169199257-0.06143433642832.1117056028658.176463523781.262673767124.661052227
24.0435857109-0.431292023665-1.418643492484.106805911362.672352022135.004292176740.2121962423480.4069566351780.223742164662-0.139107203664-0.1559992604270.3535952163730.0995430171739-0.348113131784-0.01292161870560.310422309688-0.000472971020640.0338737603940.3480137520820.04048866094310.4846264332951.383410506255.686436678714.1350024489
34.693783800050.622378365673-0.6575400798492.206253058690.4083141812613.1744234932-0.0704246577211-0.331494151226-0.4866569304890.417982635174-0.06793316050.4408087176890.544842499625-0.1430620315350.05766489107710.377232097244-0.03609074562180.06948247963960.269481595140.02379590422760.37319310319471.843485822445.933748888317.3401654226
47.36136066385-0.497116569275-0.3302306409562.891760784090.2015540940314.04026344442-0.129767901658-0.415285764510.0441935178510.5311451214660.05812647192810.1574874026710.239548601142-0.1020577332240.07038607341720.492293722382-0.06553975322940.110390049590.354128276535-0.02837929099370.30613877614370.633756053254.810984706824.1158030053
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 14 through 58 )14 - 581 - 45
22chain 'A' and (resid 59 through 209 )59 - 20946 - 186
33chain 'A' and (resid 210 through 330 )210 - 330187 - 307
44chain 'A' and (resid 331 through 391 )331 - 391308 - 368

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