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- PDB-5kck: Crystal structure of anthranilate synthase component I from Strep... -

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Basic information

Entry
Database: PDB / ID: 5kck
TitleCrystal structure of anthranilate synthase component I from Streptococcus pneumoniae TIGR4
ComponentsAnthranilate synthase component I
KeywordsLYASE / CSGID / anthranilate synthase / Structural Genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


anthranilate synthase / anthranilate synthase activity / tryptophan biosynthetic process / metal ion binding
Similarity search - Function
Anthranilate synthase component I, PabB-like / Anthranilate synthase component I, N-terminal / Anthranilate synthase component I, N terminal region / Anthranilate synthase / Anthranilate synthase / Anthranilate synthase component I-like / ADC synthase / Chorismate-utilising enzyme, C-terminal / chorismate binding enzyme / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Anthranilate synthase component 1
Similarity search - Component
Biological speciesStreptococcus pneumoniae serotype 4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsChang, C. / Michalska, K. / Bigelow, L. / Jedrzejczak, R. / ANDERSON, W.F. / JOACHIMIAK, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of anthranilate synthase component I from Streptococcus pneumoniae TIGR4
Authors: Chang, C. / Michalska, K. / Bigelow, L. / Jedrzejczak, R. / ANDERSON, W.F. / JOACHIMIAK, A.
History
DepositionJun 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Anthranilate synthase component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7003
Polymers51,5161
Non-polymers1842
Water2,558142
1
A: Anthranilate synthase component I
hetero molecules

A: Anthranilate synthase component I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,4016
Polymers103,0322
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area10480 Å2
ΔGint-50 kcal/mol
Surface area37030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.946, 86.127, 55.792
Angle α, β, γ (deg.)90.000, 93.450, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Anthranilate synthase component I


Mass: 51516.117 Da / Num. of mol.: 1 / Fragment: UNP residues 2-448
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4) (bacteria)
Strain: ATCC BAA-334 / TIGR4 / Gene: trpE, SP_1817 / Plasmid: pMCSG68
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0H2URN1, anthranilate synthase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.83 Å3/Da / Density % sol: 56.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES, 20%, PEG-8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 7, 2015
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 28979 / % possible obs: 99.3 % / Redundancy: 3.2 % / Biso Wilson estimate: 31.32 Å2 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.059 / Rrim(I) all: 0.109 / Χ2: 0.711 / Net I/av σ(I): 9.578 / Net I/σ(I): 7.5 / Num. measured all: 93202
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.242.60.495194.8
2.24-2.282.90.482197.6
2.28-2.323.10.455198.6
2.32-2.373.10.406199.9
2.37-2.423.20.391199.9
2.42-2.483.30.3491100
2.48-2.543.30.3211100
2.54-2.613.30.271100
2.61-2.683.30.2211100
2.68-2.773.30.1841100
2.77-2.873.30.1481100
2.87-2.993.30.125199.9
2.99-3.123.30.106199.9
3.12-3.293.30.092199.9
3.29-3.493.30.075199.9
3.49-3.763.30.065199.6
3.76-4.143.20.056199.6
4.14-4.733.20.049199
4.73-5.963.30.047198.8
5.96-303.30.045198.2

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Processing

Software
NameVersionClassification
PHENIXdev_2386refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→29.769 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.2
RfactorNum. reflection% reflection
Rfree0.2243 1304 4.66 %
Rwork0.1823 --
obs0.1842 28005 95.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.51 Å2 / Biso mean: 40.0362 Å2 / Biso min: 15.93 Å2
Refinement stepCycle: final / Resolution: 2.2→29.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3425 0 12 142 3579
Biso mean--57.82 42.46 -
Num. residues----435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063524
X-RAY DIFFRACTIONf_angle_d0.7564768
X-RAY DIFFRACTIONf_chiral_restr0.051530
X-RAY DIFFRACTIONf_plane_restr0.005623
X-RAY DIFFRACTIONf_dihedral_angle_d12.1392132
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1943-2.28220.3229910.24182259235073
2.2822-2.3860.31461350.22972889302492
2.386-2.51170.30151560.23482999315598
2.5117-2.6690.29471620.21830853247100
2.669-2.87490.26651460.201730873233100
2.8749-3.16390.20811470.193630893236100
3.1639-3.62110.21821730.174530693242100
3.6211-4.55950.17351350.14433115325099
4.5595-29.7720.1911590.16673109326898
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)
14.2751-0.63540.13221.18150.32432.51780.05870.03330.00780.0072-0.0588-0.152-0.13340.3172-0.00060.1746-0.044-0.00950.17990.00380.2342-9.404427.10450.5784
21.29340.36010.0891.57110.51621.71940.1538-0.1077-0.06430.1074-0.0749-0.0359-0.05510.0397-0.06650.2092-0.0028-0.00130.18780.04960.220721.884732.96179.7908
31.17790.31520.28331.168-0.64171.38210.0857-0.25130.52760.36550.05320.5638-0.3973-0.1947-0.09220.34240.01540.09630.2933-0.05030.470218.795655.35638.2275
41.24190.6449-0.59732.1071-0.72962.46720.1905-0.26940.16610.342-0.1090.1398-0.22320.0782-0.07930.2437-0.03520.00780.2467-0.01690.254822.306645.209516.8137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 38 )A0 - 38
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 247 )A39 - 247
3X-RAY DIFFRACTION3chain 'A' and (resid 248 through 330 )A248 - 330
4X-RAY DIFFRACTION4chain 'A' and (resid 331 through 447 )A331 - 447

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