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- PDB-4q1t: Crystal structure of a glutamate 5-kinase from Burkholderia thail... -

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Basic information

Entry
Database: PDB / ID: 4q1t
TitleCrystal structure of a glutamate 5-kinase from Burkholderia thailandensis
ComponentsGlutamate 5-kinase
KeywordsTRANSFERASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Seattle Structural Genomics Center for Infectious Disease / SSGCID / essential / ATP-dependent / proline biosynthesis / 5-oxoproline
Function / homology
Function and homology information


glutamate 5-kinase / glutamate 5-kinase activity / L-proline biosynthetic process / RNA binding / ATP binding / cytoplasm
Similarity search - Function
Glutamate 5-kinase / Glutamate-5-kinase domain / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / PUA domain / PUA domain / Glutamate/acetylglutamate kinase / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase ...Glutamate 5-kinase / Glutamate-5-kinase domain / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / PUA domain / PUA domain / Glutamate/acetylglutamate kinase / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase / PUA domain / Carbamate kinase / Acetylglutamate kinase-like / PUA domain profile. / PUA domain superfamily / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / PUA-like superfamily / Roll / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of a glutamate 5-kinase from Burkholderia thailandensis
Authors: Edwards, T.E. / Davies, D.R. / Abendroth, J. / Seattle Structural Genomics Center for Infectious Disease
History
DepositionApr 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutamate 5-kinase
B: Glutamate 5-kinase
C: Glutamate 5-kinase
D: Glutamate 5-kinase


Theoretical massNumber of molelcules
Total (without water)158,7094
Polymers158,7094
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12010 Å2
ΔGint-79 kcal/mol
Surface area48410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.850, 69.150, 141.680
Angle α, β, γ (deg.)90.000, 119.510, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Beg auth comp-ID: MET / Beg label comp-ID: MET / Refine code: 0

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALAA1 - 3725 - 376
21VALVALBB1 - 3725 - 376
12VALVALAA1 - 3725 - 376
22VALVALCC1 - 3725 - 376
13VALVALAA1 - 3725 - 376
23VALVALDD1 - 3725 - 376
14VALVALBB1 - 3725 - 376
24VALVALCC1 - 3725 - 376
15VALVALBB1 - 3725 - 376
25VALVALDD1 - 3725 - 376
16LEULEUCC1 - 3715 - 375
26LEULEUDD1 - 3715 - 375

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Glutamate 5-kinase / / Gamma-glutamyl kinase / GK


Mass: 39677.312 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I1143, Gamma-glutamyl kinase, proB / Production host: Escherichia coli (E. coli) / References: UniProt: Q2SZF9, glutamate 5-kinase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.04 Å3/Da / Density % sol: 39.69 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ButhA.00483.a.A1.PW33346 at 40 mg/mL against PACT screen condition F7, 0.2 M NaOAc, 0.1 M BisTris Propane pH 6.5, 20% PEG 3350 supplemented with 20% ethylene glycol as cryo-protectant, ...Details: ButhA.00483.a.A1.PW33346 at 40 mg/mL against PACT screen condition F7, 0.2 M NaOAc, 0.1 M BisTris Propane pH 6.5, 20% PEG 3350 supplemented with 20% ethylene glycol as cryo-protectant, crystal tracking ID 226003f7, unique puck ID gzd6-4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 69894 / Num. obs: 69634 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 45.726 Å2 / Rmerge(I) obs: 0.069 / Χ2: 0.96 / Net I/σ(I): 13.25
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.15-2.210.4912.8123709510499.9
2.21-2.270.3624.3122612493399.2
2.27-2.330.3324.1122707488299.4
2.33-2.40.2535.3621951470999.8
2.4-2.480.226.2421354458099.8
2.48-2.570.1737.6920763445099.8
2.57-2.670.1419.2519981428199.8
2.67-2.780.11411.0819325414299.8
2.78-2.90.112.9418284392999.8
2.9-3.040.08414.9117551377599.8
3.04-3.210.0717.6316898363899.7
3.21-3.40.05820.7915482335999.9
3.4-3.630.05422.5514942325399.6
3.63-3.930.05324.1413494296299.8
3.93-4.30.04925.6412596277299.6
4.3-4.810.04726.6911357249999.8
4.81-5.550.0526.49999222499.6
5.55-6.80.05226.088411188499.9
6.8-9.620.05227.526392146299.3
9.620.0526.68319579693

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.14data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J5T

2j5t


Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.931 / WRfactor Rfree: 0.2501 / WRfactor Rwork: 0.2252 / FOM work R set: 0.7991 / SU B: 14.421 / SU ML: 0.18 / SU R Cruickshank DPI: 0.3042 / SU Rfree: 0.2091 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.304 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2434 3519 5.1 %RANDOM
Rwork0.2193 ---
obs0.2205 69634 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.68 Å2 / Biso mean: 42.55 Å2 / Biso min: 18.16 Å2
Baniso -1Baniso -2Baniso -3
1--1.11 Å2-0 Å2-1.69 Å2
2--1.83 Å2-0 Å2
3---0.72 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9885 0 0 279 10164
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01910000
X-RAY DIFFRACTIONr_bond_other_d0.0060.029879
X-RAY DIFFRACTIONr_angle_refined_deg1.3141.96713583
X-RAY DIFFRACTIONr_angle_other_deg1.21322448
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.10351368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06823.777376
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.795151610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1221584
X-RAY DIFFRACTIONr_chiral_restr0.0750.21685
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211563
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022141
X-RAY DIFFRACTIONr_mcbond_it1.7042.5195493
X-RAY DIFFRACTIONr_mcbond_other1.7042.5195492
X-RAY DIFFRACTIONr_mcangle_it2.7973.7636842
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A182680.09
12B182680.09
21A186380.09
22C186380.09
31A181730.09
32D181730.09
41B195880.08
42C195880.08
51B180140.09
52D180140.09
61C185810.1
62D185810.1
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 273 -
Rwork0.29 4822 -
all-5095 -
obs--99.86 %
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)
10.96880.18590.02831.3189-0.20171.2133-0.0272-0.18380.060.0473-0.01640.03910.03970.19260.04360.0150.01650.02070.17420.00710.043341.431-6.775636.198
20.87930.18520.13131.20910.27730.89350.1791-0.1026-0.2417-0.1102-0.20280.12150.0454-0.28440.02380.11170.0396-0.04280.1774-0.02030.1789-2.5485-4.079825.6831
30.8964-0.6002-0.46112.00650.54871.08970.19240.1527-0.0719-0.2857-0.22680.0637-0.2093-0.00790.03440.08220.0454-0.01070.0515-0.01030.03928.01020.06799.859
40.36440.2112-0.08881.1366-1.09573.30560.0636-0.09110.03520.01380.00450.1049-0.03510.0905-0.06810.03450.01220.03160.2066-0.00360.059111.90442.01951.7039
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 372
2X-RAY DIFFRACTION2B1 - 372
3X-RAY DIFFRACTION3C1 - 372
4X-RAY DIFFRACTION4D-2 - 372

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