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- PDB-6bb9: The crystal structure of 4-amino-4-deoxychorismate lyase from Sal... -

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Basic information

Entry
Database: PDB / ID: 6bb9
TitleThe crystal structure of 4-amino-4-deoxychorismate lyase from Salmonella typhimurium LT2
Components4-amino-4-deoxychorismate lyase
KeywordsLYASE / structural genomics / The Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


aminodeoxychorismate lyase / 4-amino-4-deoxychorismate lyase activity / para-aminobenzoic acid biosynthetic process / Lyases / folic acid biosynthetic process / carboxylic acid metabolic process / pyridoxal phosphate binding / cytosol
Similarity search - Function
Aminodeoxychorismate lyase, class IV / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal ...Aminodeoxychorismate lyase, class IV / Aminotransferase, class IV, conserved site / Aminotransferases class-IV signature. / Aminotransferase class 4, branched-chain amino acid transferase, N-terminal domain / D-amino Acid Aminotransferase; Chain A, domain 2 / D-amino Acid Aminotransferase, subunit A, domain 2 / Aminotransferase class IV / Aminotransferase-like, PLP-dependent enzymes / Branched-chain-amino-acid aminotransferase-like, N-terminal / Branched-chain-amino-acid aminotransferase-like, C-terminal / Amino-transferase class IV / D-amino Acid Aminotransferase; Chain A, domain 1 / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
4-amino-4-deoxychorismate lyase / 4-amino-4-deoxychorismate lyase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.282 Å
AuthorsTan, K. / Makowska-Grzyska, M. / Nocek, B. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of HealthHHSN272201700060C United States
CitationJournal: To Be Published
Title: The crystal structure of 4-amino-4-deoxychorismate lyase from Salmonella typhimurium LT2
Authors: Tan, K. / Makowska-Grzyska, M. / Nocek, B. / Joachimiak, A.
History
DepositionOct 17, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 4-amino-4-deoxychorismate lyase
B: 4-amino-4-deoxychorismate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,94713
Polymers60,7092
Non-polymers1,23811
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7740 Å2
ΔGint-66 kcal/mol
Surface area20740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.250, 87.250, 308.949
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 4-amino-4-deoxychorismate lyase / Aminodeoxychorismate lyase


Mass: 30354.631 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: pabC, DD95_12385, STMU2UK_01164 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic
References: UniProt: A0A0M2ITI0, UniProt: Q7CQR1*PLUS, aminodeoxychorismate lyase

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Non-polymers , 5 types, 100 molecules

#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.8 Å3/Da / Density % sol: 56.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M proline, 0.1 M HEPES, 10% w/v PEG3350

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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: Dec 9, 2010 / Details: Mirror
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.28→42 Å / Num. obs: 32870 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Biso Wilson estimate: 44.74 Å2 / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.028 / Rrim(I) all: 0.08 / Χ2: 1.617 / Net I/σ(I): 37.6
Reflection shellResolution: 2.28→2.32 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.831 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1584 / CC1/2: 0.86 / Rpim(I) all: 0.307 / Rrim(I) all: 0.887 / Χ2: 1.317 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB: 1I2L

1i2l


Resolution: 2.282→41.983 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2274 1598 4.88 %random
Rwork0.1895 ---
obs0.1914 32758 99.84 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.282→41.983 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4188 0 70 89 4347
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054347
X-RAY DIFFRACTIONf_angle_d0.7785899
X-RAY DIFFRACTIONf_dihedral_angle_d17.3472598
X-RAY DIFFRACTIONf_chiral_restr0.049656
X-RAY DIFFRACTIONf_plane_restr0.004757
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2817-2.35540.33611350.25482777X-RAY DIFFRACTION100
2.3554-2.43950.27931390.25032766X-RAY DIFFRACTION100
2.4395-2.53720.26671360.23322762X-RAY DIFFRACTION100
2.5372-2.65270.27851460.23732784X-RAY DIFFRACTION100
2.6527-2.79250.29541460.23092782X-RAY DIFFRACTION100
2.7925-2.96740.26811470.23132791X-RAY DIFFRACTION100
2.9674-3.19640.26631390.21722810X-RAY DIFFRACTION100
3.1964-3.5180.22141510.1932829X-RAY DIFFRACTION100
3.518-4.02670.19791620.17262845X-RAY DIFFRACTION100
4.0267-5.07180.18711490.14442920X-RAY DIFFRACTION100
5.0718-41.990.21281480.17813094X-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)
12.58890.61270.18083.25841.08891.63410.1950.145-0.26590.17440.3422-0.85440.25120.364-0.54830.45350.0868-0.22880.4743-0.22620.848621.5687-10.9494-5.3924
22.930.8656-4.52540.3178-0.82969.3129-0.1665-0.0859-1.38560.5915-0.0179-1.68081.1177-0.0740.27950.92880.1794-0.47140.6089-0.18071.353523.5566-21.3324.678
35.3947-0.28262.95443.45781.25032.019-0.01190.0429-0.09450.29260.1189-0.07940.3802-0.1955-0.16640.5962-0.1454-0.02380.44490.0670.2462-13.5731-29.9348-21.0537
42.42730.35981.91583.49161.16551.77180.39241.44710.4002-1.02680.1781-0.3862-0.40340.00370.10770.6392-0.15770.02170.51970.10560.3707-9.7591-20.1069-30.8454
54.82070.33650.78243.08080.73131.19470.04610.3634-0.2936-0.08580.0831-0.27470.34750.0165-0.15170.4905-0.1052-0.03170.33060.0350.2469-10.6624-29.2687-25.4866
65.29423.10380.01218.77973.72267.0674-0.26260.44910.37410.5985-0.03041.57041.0355-0.79040.37410.5106-0.10330.08380.50080.10430.5194-29.6936-10.0868-14.4731
71.465-0.60340.10962.20010.9012.07530.2689-0.2479-0.01280.2735-0.0421-0.1243-0.0425-0.2164-0.19770.4351-0.0945-0.07140.27910.05930.3363-9.6276-12.2889-12.2055
86.20782.22021.61535.70170.61453.47550.0935-0.24380.03190.27150.06860.11750.2178-0.3406-0.25380.3997-0.0435-0.00090.34710.05340.3665-14.9574-4.8081-12.4921
93.1165-0.51940.43075.24130.13141.6554-0.03620.20610.1675-0.13010.12880.37160.1154-0.2064-0.0680.3859-0.1144-0.02060.41090.11270.4334-17.108-3.3305-27.1555
104.22511.0701-0.06694.9718-0.35296.69580.0976-0.11830.33850.13760.16520.4411-0.88730.0353-0.20530.3784-0.075-0.02060.31970.07050.5133-16.49984.6903-22.6198
110.5734-1.0788-0.49373.51220.75482.6120.059-0.27110.055-0.0868-0.14350.60080.1539-0.3170.00720.3223-0.07040.03440.45680.06680.5555-25.3331-4.1542-18.9509
124.3959-1.2267-1.43773.51931.75188.9538-0.32890.468-0.2869-0.2563-0.2010.91840.3736-0.97330.37120.3557-0.1379-0.02670.48920.17540.6399-29.3039-3.4069-24.4344
132.94190.54330.71683.1851-0.43342.10110.3498-0.3738-0.42150.8029-0.0301-0.38330.7198-0.1171-0.28730.9154-0.07-0.28140.40520.06170.4535-2.749-30.1859-0.4441
141.37651.8897-0.20452.3613-0.3150.815-0.1491-0.0315-0.74850.08560.3099-1.21540.68410.3349-0.25470.85530.1163-0.2450.5236-0.11890.775815.1378-27.6602-8.2051
152.42811.1490.82631.73390.88891.37390.1324-0.0179-0.01370.28180.2739-0.68160.32160.2483-0.380.45220.0056-0.17010.3486-0.08340.611210.0733-13.2194-7.6215
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 210 through 255 )
2X-RAY DIFFRACTION2chain 'B' and (resid 256 through 269 )
3X-RAY DIFFRACTION3chain 'A' and (resid 0 through 38 )
4X-RAY DIFFRACTION4chain 'A' and (resid 39 through 52 )
5X-RAY DIFFRACTION5chain 'A' and (resid 53 through 110 )
6X-RAY DIFFRACTION6chain 'A' and (resid 111 through 125 )
7X-RAY DIFFRACTION7chain 'A' and (resid 126 through 156 )
8X-RAY DIFFRACTION8chain 'A' and (resid 157 through 177 )
9X-RAY DIFFRACTION9chain 'A' and (resid 178 through 211 )
10X-RAY DIFFRACTION10chain 'A' and (resid 212 through 227 )
11X-RAY DIFFRACTION11chain 'A' and (resid 228 through 247 )
12X-RAY DIFFRACTION12chain 'A' and (resid 248 through 269 )
13X-RAY DIFFRACTION13chain 'B' and (resid 1 through 100 )
14X-RAY DIFFRACTION14chain 'B' and (resid 101 through 125 )
15X-RAY DIFFRACTION15chain 'B' and (resid 126 through 209 )

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