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- PDB-1rd5: Crystal structure of Tryptophan synthase alpha chain homolog BX1:... -

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Basic information

Entry
Database: PDB / ID: 1rd5
TitleCrystal structure of Tryptophan synthase alpha chain homolog BX1: a member of the chemical plant defense system
ComponentsTryptophan synthase alpha chain, chloroplast
KeywordsLYASE / hydroxamic acid / DIBOA / DIMBOA / indole / indole-glycerol-phosphate
Function / homology
Function and homology information


indole-3-glycerol-phosphate lyase / indole-3-glycerol-phosphate lyase activity / tryptophan synthase / tryptophan synthase activity / L-tryptophan biosynthetic process / chloroplast / cytosol
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
MALONIC ACID / Indole-3-glycerol phosphate lyase, chloroplastic
Similarity search - Component
Biological speciesZea mays (maize)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å
AuthorsKulik, V. / Hartmann, E. / Weyand, M. / Frey, M. / Gierl, A. / Niks, D. / Dunn, M.F. / Schlichting, I.
Citation
Journal: J.Mol.Biol. / Year: 2005
Title: On the structural basis of the catalytic mechanism and the regulation of the alpha subunit of tryptophan synthase from Salmonella typhimurium and BX1 from maize, two evolutionarily related enzymes.
Authors: Kulik, V. / Hartmann, E. / Weyand, M. / Frey, M. / Gierl, A. / Niks, D. / Dunn, M.F. / Schlichting, I.
#1: Journal: Science / Year: 1997
Title: Analysis of a chemical plant defense mechanism in grasses
Authors: Frey, M. / Chomet, P. / Glawischnig, E. / Stettner, C. / Grun, S. / Winklmair, A. / Eisenreich, W. / Bacher, A. / Meeley, R.B. / Briggs, S.P. / Simcox, K. / Gierl, A.
History
DepositionNov 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Apr 29, 2015Group: Non-polymer description
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.5Dec 21, 2022Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.6May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 999SEQUENCE AUTHORS INFORMED THAT THEIR SEQUENCE IS CORRECT AT THE POSITIONS WHERE IT CONFLICTS WITH ...SEQUENCE AUTHORS INFORMED THAT THEIR SEQUENCE IS CORRECT AT THE POSITIONS WHERE IT CONFLICTS WITH THE SWISS PROT SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan synthase alpha chain, chloroplast
B: Tryptophan synthase alpha chain, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,2634
Polymers56,0552
Non-polymers2082
Water4,468248
1
A: Tryptophan synthase alpha chain, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1322
Polymers28,0281
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tryptophan synthase alpha chain, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1322
Polymers28,0281
Non-polymers1041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Tryptophan synthase alpha chain, chloroplast
B: Tryptophan synthase alpha chain, chloroplast
hetero molecules

A: Tryptophan synthase alpha chain, chloroplast
B: Tryptophan synthase alpha chain, chloroplast
hetero molecules

A: Tryptophan synthase alpha chain, chloroplast
B: Tryptophan synthase alpha chain, chloroplast
hetero molecules

A: Tryptophan synthase alpha chain, chloroplast
B: Tryptophan synthase alpha chain, chloroplast
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,05316
Polymers224,2208
Non-polymers8328
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area22160 Å2
ΔGint-143 kcal/mol
Surface area74380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)91.094, 159.815, 162.877
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-409-

HOH

21B-330-

HOH

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Components

#1: Protein Tryptophan synthase alpha chain, chloroplast / BX1 / tryptophan synthase alpha homolog


Mass: 28027.549 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Zea mays (maize) / Production host: Escherichia coli (E. coli) / References: UniProt: P42390, tryptophan synthase
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / 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: 2.64 Å3/Da / Density % sol: 53.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: Malonate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 7, 2001
RadiationProtocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→45 Å / Num. obs: 37043 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rsym value: 0.078 / Net I/σ(I): 13.8
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.7 % / Rsym value: 0.34 / % possible all: 52.7

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
MAR345data collection
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.02→25 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.305 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.235 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29867 1851 5 %RANDOM
Rwork0.24545 ---
obs0.24804 35151 100 %-
all-35151 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å20 Å20 Å2
2---0.57 Å20 Å2
3----0.33 Å2
Refine analyzeLuzzati coordinate error obs: 0.259 Å
Refinement stepCycle: LAST / Resolution: 2.02→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 14 248 4058
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0460.0223908
X-RAY DIFFRACTIONr_bond_other_d0.0020.023740
X-RAY DIFFRACTIONr_angle_refined_deg3.0211.995300
X-RAY DIFFRACTIONr_angle_other_deg1.69538714
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3215505
X-RAY DIFFRACTIONr_chiral_restr0.2060.2624
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.024283
X-RAY DIFFRACTIONr_gen_planes_other0.0110.02700
X-RAY DIFFRACTIONr_nbd_refined0.2470.2757
X-RAY DIFFRACTIONr_nbd_other0.2520.24074
X-RAY DIFFRACTIONr_nbtor_other0.110.22294
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.2194
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3130.29
X-RAY DIFFRACTIONr_mcbond_it1.7761.52537
X-RAY DIFFRACTIONr_mcangle_it2.76324090
X-RAY DIFFRACTIONr_scbond_it4.55331371
X-RAY DIFFRACTIONr_scangle_it7.0324.51210
LS refinement shellResolution: 2.02→2.068 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.688 76
Rwork0.512 1234
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)
11.78890.6967-0.26392.48370.67862.2384-0.02480.0689-0.0658-0.0703-0.0095-0.06320.08370.0190.03430.07840.01530.04720.05240.02140.031440.49823.25117.895
22.349-0.2828-0.33731.96420.89761.4619-0.08490.25160.1003-0.2520.05360.0719-0.1321-0.04540.03130.093-0.0426-0.00190.05130.02780.06275.69317.27327.873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2622 - 262
2X-RAY DIFFRACTION2BB2 - 582 - 58
3X-RAY DIFFRACTION2BB61 - 17561 - 175
4X-RAY DIFFRACTION2BB187 - 262187 - 262

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