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- PDB-4dhe: Crystal structure of a probable GTP-binding protein engB from Bur... -

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Basic information

Entry
Database: PDB / ID: 4dhe
TitleCrystal structure of a probable GTP-binding protein engB from Burkholderia thailandensis
ComponentsProbable GTP-binding protein EngB
KeywordsCELL CYCLE / melioidosis / RAS-like GTPase / cell division / septation / GTP-binding / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


division septum assembly / GTP binding / metal ion binding / cytosol
Similarity search - Function
GTP-binding protein, ribosome biogenesis, YsxC / EngB-type guanine nucleotide-binding (G) domain profile. / EngB-type guanine nucleotide-binding (G) domain / 50S ribosome-binding GTPase / GTP binding domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Probable GTP-binding protein EngB
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionJan 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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: Probable GTP-binding protein EngB
B: Probable GTP-binding protein EngB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1835
Polymers49,0762
Non-polymers1063
Water2,900161
1
A: Probable GTP-binding protein EngB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6444
Polymers24,5381
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable GTP-binding protein EngB


Theoretical massNumber of molelcules
Total (without water)24,5381
Polymers24,5381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.940, 76.960, 134.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: _ / Auth seq-ID: -1 - 206 / Label seq-ID: 3 - 210

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Probable GTP-binding protein EngB


Mass: 24538.080 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: BTH_I3037, engB / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2SU58
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 2.58 Å3/Da / Density % sol: 52.3 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: ButhA.00252.a.A1.PW33397 at 34 mg/mL against JCSG+ H8, 0.2 M NaCl, 0.1 M BisTris, 25% PEG 3350 with 15% EG as cryo-protectant, Crystal tracking ID 225992h8, pH 5.5, VAPOR DIFFUSION, SITTING ...Details: ButhA.00252.a.A1.PW33397 at 34 mg/mL against JCSG+ H8, 0.2 M NaCl, 0.1 M BisTris, 25% PEG 3350 with 15% EG as cryo-protectant, Crystal tracking ID 225992h8, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 26548 / Num. obs: 26282 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Biso Wilson estimate: 36.759 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 13.31
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.2-2.260.4972.998528190698.8
2.26-2.320.4733.28907187099
2.32-2.390.4083.88929180299
2.39-2.460.3734.389209177299.3
2.46-2.540.3185.289306172599.5
2.54-2.630.2985.79245166299.8
2.63-2.730.2476.99168161999.8
2.73-2.840.2048.298925154899.5
2.84-2.970.179.768632149499.8
2.97-3.110.12712.478276143099.5
3.11-3.280.115.477821136699.6
3.28-3.480.07819.347281127799
3.48-3.720.06322.876661120298.8
3.72-4.020.05525.526218113498.6
4.02-4.40.04630.775694103998
4.4-4.920.04333.27523596798.9
4.92-5.680.04629.48459185398.7
5.68-6.960.04230.42418573799.3
6.96-9.840.0337.49325758599.3
9.840.02442.94152029483.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.78 Å
Translation3 Å19.78 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1pui

1pui


Resolution: 2.2→19.781 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.91 / WRfactor Rfree: 0.2384 / WRfactor Rwork: 0.2057 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.778 / SU B: 14.927 / SU ML: 0.196 / SU R Cruickshank DPI: 0.2702 / SU Rfree: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.22 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES WITH TLS ADDED. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2738 1334 5.1 %RANDOM
Rwork0.2349 ---
obs0.2368 26281 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 82.16 Å2 / Biso mean: 37.8454 Å2 / Biso min: 14.96 Å2
Baniso -1Baniso -2Baniso -3
1--2.07 Å20 Å20 Å2
2--5.34 Å20 Å2
3----3.27 Å2
Refinement stepCycle: LAST / Resolution: 2.2→19.781 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 3 161 3194
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.023100
X-RAY DIFFRACTIONr_bond_other_d0.0040.022044
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9594220
X-RAY DIFFRACTIONr_angle_other_deg1.16534984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4895395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.50723.333126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72115481
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8971519
X-RAY DIFFRACTIONr_chiral_restr0.0780.2484
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213464
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02635
Refine LS restraints NCS

Ens-ID: 1 / Number: 5903 / Refine-ID: X-RAY DIFFRACTION / Type: LOCAL / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 95 -
Rwork0.31 1651 -
all-1746 -
obs--98.64 %
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)
10.59870.0422-0.0150.59760.38770.9548-0.0173-0.0913-0.1676-0.0276-0.0448-0.0430.0299-0.03150.0620.2956-0.0020.01140.0204-0.00280.28220.05398.1347-2.8587
21.1484-0.1574-0.52781.07640.73240.6572-0.2006-0.3986-0.0979-0.01590.16470.06980.03850.2760.03590.31080.0615-0.05340.1684-0.00440.2185-7.266714.69744.4704
31.4670.2095-0.06580.19010.34190.8674-0.08760.3881-0.13690.0298-0.0075-0.0054-0.0474-0.13670.09520.26790.0026-0.02470.143-0.04680.2152-6.365812.189-13.8182
40.1019-0.31520.45561.1498-1.55242.1551-0.06990.02670.0570.111-0.1297-0.1058-0.23920.14580.19960.16740.0271-0.07370.51790.19590.16818.544641.6331-26.979
50.21140.3940.45691.5213-0.35034.268-0.27230.0870.1316-0.2317-0.05290.1505-0.11360.29840.32510.2295-0.0449-0.09010.52920.27960.188116.51638.4079-31.45
61.18980.60840.61271.2296-0.39060.9181-0.00560.34-0.01060.05560.0013-0.06760.02550.16760.00430.1525-0.0340.02780.40750.04430.127318.84624.6726-22.7217
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 47
2X-RAY DIFFRACTION2A48 - 65
3X-RAY DIFFRACTION3A66 - 206
4X-RAY DIFFRACTION4B-1 - 36
5X-RAY DIFFRACTION5B37 - 85
6X-RAY DIFFRACTION6B95 - 206

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