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- PDB-3vaa: 1.7 Angstrom Resolution Crystal Structure of Shikimate Kinase fro... -

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Basic information

Entry
Database: PDB / ID: 3vaa
Title1.7 Angstrom Resolution Crystal Structure of Shikimate Kinase from Bacteroides thetaiotaomicron
ComponentsShikimate kinase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / metal binding
Function / homology
Function and homology information


shikimate kinase / shikimate kinase activity / shikimate metabolic process / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
Shikimate kinase/Threonine synthase-like 1 / Shikimate kinase/gluconokinase / Shikimate kinase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / DI(HYDROXYETHYL)ETHER / Shikimate kinase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMinasov, G. / Light, S.H. / Halavaty, A. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.7 Angstrom Resolution Crystal Structure of Shikimate Kinase from Bacteroides thetaiotaomicron.
Authors: Minasov, G. / Light, S.H. / Halavaty, A. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 29, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
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_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_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: Shikimate kinase
B: Shikimate kinase
C: Shikimate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,53311
Polymers69,8203
Non-polymers7138
Water8,161453
1
A: Shikimate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5504
Polymers23,2731
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Shikimate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,5364
Polymers23,2731
Non-polymers2623
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Shikimate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4483
Polymers23,2731
Non-polymers1742
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.253, 46.460, 105.124
Angle α, β, γ (deg.)90.00, 97.42, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Shikimate kinase / SK


Mass: 23273.385 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: aroK, BT_3393 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic / References: UniProt: Q8A2B2, shikimate kinase

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Non-polymers , 5 types, 461 molecules

#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 7.5 mg/mL, 0.25M Sodium chloride, Tris-HCl pH 8.3, Screen: Classics II (C9), 1.1M Sodium malonate, 0.1M HEPES pH 7.0, 0.5% (v/v) Jeffamine ED-2001, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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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 225 mm CCD / Detector: CCD / Date: Dec 9, 2011 / Details: Beryllium lenses
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 64576 / Num. obs: 64576 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 25.8 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 17.8
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.495 / Mean I/σ(I) obs: 2.09 / Num. unique all: 3002 / % possible all: 93.8

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PT5

2pt5


Resolution: 1.7→29.06 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.958 / SU B: 4.111 / SU ML: 0.062
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.098 / ESU R Free: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19923 3268 5.1 %RANDOM
Rwork0.16348 ---
all0.16527 61285 --
obs0.16527 61285 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.505 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å2-0.46 Å2
2--0.71 Å2-0 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4295 0 42 453 4790
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224582
X-RAY DIFFRACTIONr_bond_other_d0.0010.023216
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.966186
X-RAY DIFFRACTIONr_angle_other_deg0.8153.0017755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.1255554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.43223.77252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.83315818
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7451542
X-RAY DIFFRACTIONr_chiral_restr0.0840.2650
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025183
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021025
X-RAY DIFFRACTIONr_mcbond_it1.0141.52689
X-RAY DIFFRACTIONr_mcbond_other0.3491.51097
X-RAY DIFFRACTIONr_mcangle_it1.81924345
X-RAY DIFFRACTIONr_scbond_it3.17431893
X-RAY DIFFRACTIONr_scangle_it5.0014.51839
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.263 204 -
Rwork0.253 4225 -
obs-4225 93.05 %
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)
12.2723-0.13550.67812.17350.83663.51450.03420.0542-0.1637-0.2339-0.0052-0.10240.1530.4556-0.0290.16760.0305-0.00820.06830.00340.034114.4224-10.79466.1602
21.92610.2185-0.0221.74071.3718.44280.2706-0.0455-0.3188-0.1249-0.1916-0.150.46420.4338-0.0790.18340.0652-0.0490.1196-0.02230.189718.1286-16.835811.9485
35.8015-0.3188-0.224311.35452.86441.02410.2205-0.3089-0.11660.8905-0.45860.43220.3334-0.38040.23810.2899-0.19290.00730.3237-0.05370.14986.2485-16.911926.4309
40.96730.10190.67121.52911.26154.64490.089-0.00180.0572-0.1856-0.1196-0.0584-0.11170.16380.03060.0768-0.0101-0.02120.0878-0.0120.067814.6844-5.411217.2002
51.76350.3140.28571.69060.39561.6342-0.0840.06090.0542-0.1745-0.00560.16220.0572-0.03510.08960.20580.0059-0.05580.0322-0.00450.07742.7477-10.3041.8283
61.250.64020.04450.7439-0.01531.7353-0.028-0.0060.02010.04530.0329-0.06490.07930.083-0.00490.01380.0084-0.00910.0162-0.00910.03726.53343.899840.9538
74.1449-0.615-1.92183.42160.8913.1828-0.11220.1543-0.15380.285-0.0240.45080.1478-0.34290.13620.0632-0.0350.01290.09050.01720.078611.57121.47338.7787
81.98611.87733.75964.7286-2.767821.42170.7768-0.57940.06231.7672-1.3191-0.3558-0.95751.39470.54230.9305-0.1972-0.1870.9803-0.19530.649110.140711.294450.6594
91.7361-0.7731-0.73282.90410.60322.37970.0230.05380.1042-0.0163-0.0010.174-0.094-0.2443-0.0220.0267-0.0229-0.02280.120300.082110.99455.901434.5019
107.11570.6192-4.208711.091-2.817110.10690.1646-0.1145-0.29130.0910.02430.26180.8434-0.4354-0.18890.2505-0.1285-0.05510.06720.0280.051712.7482-14.030939.9111
113.9353-1.27590.33222.40210.23473.3055-0.1259-0.1188-0.00980.08430.1456-0.1502-0.01670.2803-0.01970.0331-0.03830.01720.1299-0.00110.072250.222414.875739.3177
121.63830.38360.16211.5694-0.44930.9518-0.14470.1994-0.2391-0.23610.0811-0.13930.08020.03170.06350.0452-0.03810.03840.1198-0.06190.064356.326411.154125.9889
133.612-0.36970.46336.78920.01183.3592-0.11070.32030.438-0.22370.0097-0.1001-0.64710.15480.1010.1575-0.0774-0.00560.13130.04790.117143.114122.526131.3486
142.9950.9391-0.00722.38660.41833.6152-0.16450.5190.4368-0.41780.14970.1678-0.6559-0.03760.01480.1777-0.0401-0.02060.16470.08480.115640.8622.488526.0143
154.49592.15860.43175.82730.92193.49510.1279-0.25510.20980.1434-0.0319-0.0272-0.25430.1068-0.09590.0337-0.03480.01960.0886-0.04520.027143.659920.454547.3069
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 22
2X-RAY DIFFRACTION2A23 - 39
3X-RAY DIFFRACTION3A40 - 54
4X-RAY DIFFRACTION4A55 - 98
5X-RAY DIFFRACTION5A99 - 175
6X-RAY DIFFRACTION6B0 - 92
7X-RAY DIFFRACTION7B93 - 113
8X-RAY DIFFRACTION8B114 - 126
9X-RAY DIFFRACTION9B127 - 156
10X-RAY DIFFRACTION10B157 - 175
11X-RAY DIFFRACTION11C0 - 27
12X-RAY DIFFRACTION12C28 - 92
13X-RAY DIFFRACTION13C93 - 121
14X-RAY DIFFRACTION14C122 - 156
15X-RAY DIFFRACTION15C157 - 175

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