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- PDB-4neg: The crystal structure of tryptophan synthase subunit beta from Ba... -

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Basic information

Entry
Database: PDB / ID: 4neg
TitleThe crystal structure of tryptophan synthase subunit beta from Bacillus anthracis str. 'Ames Ancestor'
ComponentsTryptophan synthase beta chain
KeywordsLYASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID / NIAID / National Institute of Allergy and Infectious Diseases
Function / homology
Function and homology information


L-tryptophan metabolic process / tryptophan synthase / tryptophan synthase activity / cytoplasm
Similarity search - Function
Tryptophan synthase, beta chain, conserved site / Tryptophan synthase, beta chain / Tryptophan synthase beta chain/beta chain-like / Tryptophan synthase beta chain pyridoxal-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Tryptophan synthase beta chain
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.201 Å
AuthorsTan, K. / Zhang, R. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: The crystal structure of tryptophan synthase subunit beta from Bacillus anthracis str. 'Ames Ancestor'
Authors: Tan, K. / Zhang, R. / Zhou, M. / Kwon, K. / Anderson, W.F. / Joachimiak, A.
History
DepositionOct 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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: Tryptophan synthase beta chain
B: Tryptophan synthase beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6198
Polymers89,1472
Non-polymers4726
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-17 kcal/mol
Surface area25000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.762, 49.037, 76.494
Angle α, β, γ (deg.)90.00, 99.35, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tryptophan synthase beta chain


Mass: 44573.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames Ancestor / Gene: Bacillus anthracis, BAS1161, BA_1253, GBAA_1253, trpB / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)majic / References: UniProt: Q81TL8, tryptophan synthase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH2O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / 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: 2.08 Å3/Da / Density % sol: 40.97 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M Li2SO4, 0.1M Tris, 25%(w/v) PEG 400, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935, 0.97935, 0.97945
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 2, 2013 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979351
20.979451
ReflectionResolution: 2.2→45.5 Å / Num. all: 37647 / Num. obs: 37647 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -5 / Redundancy: 4.8 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 15.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.623 / Mean I/σ(I) obs: 2.03 / Num. unique all: 1881 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.201→44.885 Å / SU ML: 0.26 / σ(F): 1.34 / Phase error: 27.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2172 1877 5 %random
Rwork0.175 ---
all0.1772 37568 --
obs0.1772 37568 99.49 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.201→44.885 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4785 0 27 75 4887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074888
X-RAY DIFFRACTIONf_angle_d1.0336604
X-RAY DIFFRACTIONf_dihedral_angle_d13.521743
X-RAY DIFFRACTIONf_chiral_restr0.066750
X-RAY DIFFRACTIONf_plane_restr0.005848
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.201-2.260.31051360.25312669X-RAY DIFFRACTION97
2.26-2.32650.2751390.2272744X-RAY DIFFRACTION99
2.3265-2.40160.26391370.21122686X-RAY DIFFRACTION99
2.4016-2.48750.25421380.20542745X-RAY DIFFRACTION100
2.4875-2.5870.27761450.20972762X-RAY DIFFRACTION100
2.587-2.70480.24841200.19742725X-RAY DIFFRACTION100
2.7048-2.84740.29621490.20322724X-RAY DIFFRACTION100
2.8474-3.02570.23281500.19722759X-RAY DIFFRACTION100
3.0257-3.25930.26831440.19752761X-RAY DIFFRACTION100
3.2593-3.58710.22981360.17412752X-RAY DIFFRACTION100
3.5871-4.10590.17911790.15192738X-RAY DIFFRACTION100
4.1059-5.17180.16331400.13352797X-RAY DIFFRACTION100
5.1718-44.89420.20281640.17022829X-RAY DIFFRACTION99
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)
13.6493-1.45010.16061.6907-0.51961.93790.11760.3382-0.1267-0.1999-0.14480.29660.0488-0.2403-0.01310.2997-0.03260.00920.3227-0.11270.3609-35.582-2.7022-15.4972
25.9759-1.4363-0.75674.8389-0.08173.56460.3682-0.11290.6777-0.057-0.17190.0807-0.3516-0.2796-0.18270.35340.0590.06610.4516-0.06270.4486-41.281214.0467-15.2795
38.3376-7.51110.74439.4347-1.88911.79110.1427-0.1331-0.4335-0.396-0.02030.55430.2726-0.3378-0.08990.2956-0.07690.01430.3555-0.09310.3107-35.4014-9.3337-10.5291
44.1960.752-1.04462.8295-0.94362.79070.0817-0.34560.31810.1099-0.030.3147-0.1275-0.1883-0.06430.271-0.01410.01950.3962-0.10330.2738-26.4485-2.33220.3506
56.0735.96464.74477.38343.78196.1656-0.10621.0274-1.2707-0.03150.334-0.46140.37061.1544-0.1790.44760.13690.07950.76560.04970.47611.4722-10.4976-22.9959
65.7372-5.7021-4.69925.66054.66993.8631-0.00580.1527-1.4005-0.345-0.04040.1210.5599-0.0710.04990.4466-0.00330.04320.3913-0.0160.5454-9.111-15.3515-20.2964
78.2742-4.16465.93954.5703-4.49476.4910.09970.3271-0.0378-0.3040.09090.1276-0.3115-0.7539-0.2850.32860.09820.01040.5461-0.05150.26-25.83361.1595-31.8523
85.39490.6764-0.02623.69670.66333.34260.18650.2330.7511-0.2139-0.2889-0.273-0.30750.38270.07360.2836-0.00520.03690.43770.08380.34710.27853.1635-16.792
95.89721.54984.36882.8002-0.82636.52190.16570.6894-0.1694-0.136-0.19740.09610.36020.35590.00810.35780.08720.03420.4975-0.07340.316-12.8396-7.5247-32.4171
104.0991-0.0095-3.2978.1473-3.12015.29050.3380.8152-0.1282-0.2507-0.397-0.81660.19320.29970.02910.40.11120.05530.8292-0.04970.3451-12.9853-0.8031-40.0629
115.16480.0044-0.23673.12710.68515.75610.35680.53890.4795-0.3340.1476-0.15-0.8572-0.0025-0.49520.47850.0960.13630.54110.12720.4699-20.171110.2264-35.4438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 103 )
2X-RAY DIFFRACTION2chain 'A' and (resid 104 through 200 )
3X-RAY DIFFRACTION3chain 'A' and (resid 201 through 224 )
4X-RAY DIFFRACTION4chain 'A' and (resid 225 through 394 )
5X-RAY DIFFRACTION5chain 'B' and (resid 19 through 37 )
6X-RAY DIFFRACTION6chain 'B' and (resid 38 through 54 )
7X-RAY DIFFRACTION7chain 'B' and (resid 55 through 84 )
8X-RAY DIFFRACTION8chain 'B' and (resid 85 through 200 )
9X-RAY DIFFRACTION9chain 'B' and (resid 201 through 224 )
10X-RAY DIFFRACTION10chain 'B' and (resid 225 through 261 )
11X-RAY DIFFRACTION11chain 'B' and (resid 262 through 392 )

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