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- PDB-3fbt: Crystal structure of a chorismate mutase/shikimate 5-dehydrogenas... -

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Basic information

Entry
Database: PDB / ID: 3fbt
TitleCrystal structure of a chorismate mutase/shikimate 5-dehydrogenase fusion protein from Clostridium acetobutylicum
Componentschorismate mutase and shikimate 5-dehydrogenase fusion protein
KeywordsOXIDOREDUCTASE / LYASE / STRUCTURAL GENOMICS / Amino-acid biosynthesis / Aromatic amino acid biosynthesis / NADP / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / shikimate metabolic process / chorismate mutase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NADP binding
Similarity search - Function
Chorismate mutase, Gram-positive / Shikimate dehydrogenase / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Shikimate dehydrogenase family ...Chorismate mutase, Gram-positive / Shikimate dehydrogenase / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Shikimate dehydrogenase family / Chorismate mutase type II / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Shikimate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsBonanno, J.B. / Gilmore, M. / Bain, K.T. / Hu, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a chorismate mutase/shikimate 5-dehydrogenase fusion protein from Clostridium acetobutylicum
Authors: Bonanno, J.B. / Gilmore, M. / Bain, K.T. / Hu, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionNov 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: chorismate mutase and shikimate 5-dehydrogenase fusion protein
B: chorismate mutase and shikimate 5-dehydrogenase fusion protein
C: chorismate mutase and shikimate 5-dehydrogenase fusion protein
D: chorismate mutase and shikimate 5-dehydrogenase fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,76313
Polymers126,8984
Non-polymers8659
Water2,756153
1
A: chorismate mutase and shikimate 5-dehydrogenase fusion protein
B: chorismate mutase and shikimate 5-dehydrogenase fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,9297
Polymers63,4492
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-96 kcal/mol
Surface area24180 Å2
MethodPISA
2
C: chorismate mutase and shikimate 5-dehydrogenase fusion protein
D: chorismate mutase and shikimate 5-dehydrogenase fusion protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8336
Polymers63,4492
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-77 kcal/mol
Surface area23790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.132, 135.336, 67.140
Angle α, β, γ (deg.)90.000, 102.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
chorismate mutase and shikimate 5-dehydrogenase fusion protein


Mass: 31724.502 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: aro, CA_C0897 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q97KM0, chorismate mutase, shikimate dehydrogenase (NADP+)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 153 / 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: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6
Details: 100mM Bis-Tris pH 6.0, 31% PEG 3350, 200mM ammonium sulfate, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 14, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.1→67.729 Å / Num. all: 66193 / Num. obs: 62486 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.083 / Net I/σ(I): 10.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.407 / Mean I/σ(I) obs: 3.1 / Num. measured all: 45323 / Num. unique all: 8818 / Rsym value: 0.407 / % possible all: 92.3

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.902 / WRfactor Rfree: 0.541 / WRfactor Rwork: 0.691 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.738 / SU B: 6.816 / SU ML: 0.183 / SU R Cruickshank DPI: 0.298 / SU Rfree: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.298 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.299 3154 5.1 %RANDOM
Rwork0.233 ---
obs0.236 62385 94.41 %-
all-66079 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 94.43 Å2 / Biso mean: 50.548 Å2 / Biso min: 29.08 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20.64 Å2
2--0.56 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8391 0 45 153 8589
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0228569
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.98311558
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32751077
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.90725.601341
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.704151586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8771517
X-RAY DIFFRACTIONr_chiral_restr0.1230.21323
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216197
X-RAY DIFFRACTIONr_mcbond_it1.1151.55346
X-RAY DIFFRACTIONr_mcangle_it1.96428627
X-RAY DIFFRACTIONr_scbond_it3.12433223
X-RAY DIFFRACTIONr_scangle_it5.0514.52930
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 233 -
Rwork0.306 4193 -
all-4426 -
obs-4193 92.32 %

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