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- PDB-4rpf: Crystal structure of homoserine kinase from Yersinia pestis Nepal... -

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Basic information

Entry
Database: PDB / ID: 4rpf
TitleCrystal structure of homoserine kinase from Yersinia pestis Nepal516, NYSGRC target 032715
ComponentsHomoserine kinase
KeywordsTRANSFERASE / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NYSGRC / KINASE
Function / homology
Function and homology information


homoserine kinase / homoserine kinase activity / threonine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Homoserine kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 ...Homoserine kinase / GHMP kinase, ATP-binding, conserved site / GHMP kinases putative ATP-binding domain. / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
CITRIC ACID / Homoserine kinase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsPtskovsky, Y. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. ...Ptskovsky, Y. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal Structure of Homoserine Kinase from Yersinia Pestis Nepal516, Nysgrc Target 032715
Authors: Patskovsky, Y. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / ...Authors: Patskovsky, Y. / Bhosle, R. / Toro, R. / Hillerich, B. / Gizzi, A. / Garforth, S. / Kar, A. / Chan, M.K. / Lafluer, J. / Patel, H. / Matikainen, B. / Chamala, S. / Lim, S. / Celikgil, A. / Villegas, G. / Evans, B. / Love, J. / Fiser, A. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
History
DepositionOct 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Homoserine kinase
B: Homoserine kinase
C: Homoserine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,6186
Polymers100,0423
Non-polymers5763
Water1,67593
1
A: Homoserine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5392
Polymers33,3471
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Homoserine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5392
Polymers33,3471
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Homoserine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5392
Polymers33,3471
Non-polymers1921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Homoserine kinase
B: Homoserine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0794
Polymers66,6952
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-11 kcal/mol
Surface area23560 Å2
MethodPISA
5
C: Homoserine kinase
hetero molecules

C: Homoserine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,0794
Polymers66,6952
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area3840 Å2
ΔGint-10 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.861, 93.659, 107.617
Angle α, β, γ (deg.)90.00, 90.14, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.49539, -0.868654, 0.005348), (-0.868671, -0.495383, 0.002749), (0.000261, -0.006007, -0.999982)40.59843, 70.19075, 143.72435
3given(0.502252, 0.864703, 0.005613), (0.864721, -0.502243, -0.003061), (0.000172, 0.006391, -0.99998)-41.5091, -22.74228, 179.12292

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Components

#1: Protein Homoserine kinase / / HK / HSK


Mass: 33347.250 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: Nepal516 / Gene: thrB, YPN_0332, YP516_0338 / Plasmid: PET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q1CMW6, homoserine kinase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 4.13 Å3/Da / Density % sol: 70.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PROTEIN IN 10 MM BIS-TRIS, 500 MM SODIUM CHLORIDE, 10% GLYCEROL, 5 MM DTT, 10 MM D-GLUCOSE, RESERVOIR: 0.17 M AMMONIUM ACETATE, 0.085 M SODIUM CITRATE, PH 5.6, 25.5% W/V PEG4000, 15% W/V ...Details: PROTEIN IN 10 MM BIS-TRIS, 500 MM SODIUM CHLORIDE, 10% GLYCEROL, 5 MM DTT, 10 MM D-GLUCOSE, RESERVOIR: 0.17 M AMMONIUM ACETATE, 0.085 M SODIUM CITRATE, PH 5.6, 25.5% W/V PEG4000, 15% W/V GLYCEROL, 0.5 M 2-Aminoethylphosphonate; CRYOPROTECTANT = RESERVOIR, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2014 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.49
111/2H-3/2K, -1/2H-1/2K, -L20.328
111/2H+3/2K, 1/2H-1/2K, -L30.182
ReflectionResolution: 2.3→50 Å / Num. obs: 70518 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Rmerge(I) obs: 0.084 / Rsym value: 0.084 / Net I/σ(I): 18.25
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 6 % / Mean I/σ(I) obs: 1.5 / % possible all: 97.9

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Processing

Software
NameVersionClassification
SHELXmodel building
BUCCANEERmodel building
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.3→40.72 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.904 / SU B: 5.054 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.051 / ESU R Free: 0.047 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29054 2024 2.9 %RANDOM
Rwork0.24038 ---
obs0.24189 68460 97.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 57.805 Å2
Baniso -1Baniso -2Baniso -3
1--23.95 Å2-0 Å220.42 Å2
2--26.76 Å20 Å2
3----2.81 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6982 0 39 93 7114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0197172
X-RAY DIFFRACTIONr_bond_other_d0.0010.026789
X-RAY DIFFRACTIONr_angle_refined_deg1.1091.9619722
X-RAY DIFFRACTIONr_angle_other_deg0.732315605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2775928
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.18624.408304
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.186151158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8371540
X-RAY DIFFRACTIONr_chiral_restr0.0630.21069
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218299
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021627
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it19.48210.9443715
X-RAY DIFFRACTIONr_mcbond_other19.48310.9423714
X-RAY DIFFRACTIONr_mcangle_it18.68216.4114639
X-RAY DIFFRACTIONr_mcangle_other18.68116.4134640
X-RAY DIFFRACTIONr_scbond_it23.06512.0063457
X-RAY DIFFRACTIONr_scbond_other23.07112.0083455
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other22.01617.5635082
X-RAY DIFFRACTIONr_long_range_B_refined22.63932.9478009
X-RAY DIFFRACTIONr_long_range_B_other22.63832.9478010
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.295→2.355 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 79 -
Rwork0.213 4201 -
obs--80.5 %

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