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- PDB-2d8e: Structure of Chorismate Mutase (Form II) from Thermus Thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2d8e
TitleStructure of Chorismate Mutase (Form II) from Thermus Thermophilus HB8
Componentsphospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase
KeywordsISOMERASE / Chorismate Mutase / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


chorismate metabolic process / chorismate mutase / chorismate mutase activity / 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aldehyde-lyase activity / aromatic amino acid family biosynthetic process
Similarity search - Function
Chorismate mutase, Firmicutes/Deinococcus / Phospho-2-dehydro-3-deoxyheptonate aldolase, subtype 2 / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type ...Chorismate mutase, Firmicutes/Deinococcus / Phospho-2-dehydro-3-deoxyheptonate aldolase, subtype 2 / : / Chorismate mutase / Chorismate Mutase Domain, subunit A / Chorismate mutase domain superfamily / Chorismate mutase domain profile. / Chorismate mutase type II / Chorismate mutase type II superfamily / Chorismate mutase II, prokaryotic-type / Chorismate mutase type II / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase-type TIM barrel / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase / Phospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBagautdinov, B. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure of Chorismate Mutase from Thermus Thermophilus HB8
Authors: Bagautdinov, B. / Kunishima, N.
History
DepositionDec 2, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 2, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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

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Assembly

Deposited unit
A: phospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase


Theoretical massNumber of molelcules
Total (without water)10,7381
Polymers10,7381
Non-polymers00
Water1,26170
1
A: phospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase

A: phospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase


Theoretical massNumber of molelcules
Total (without water)21,4762
Polymers21,4762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4940 Å2
ΔGint-47 kcal/mol
Surface area9730 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.898, 71.061, 49.370
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-147-

HOH

DetailsThe biological assembly is a dimer

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Components

#1: Protein phospho-2-dehydro-3-deoxyheptonate aldolase/chorismate mutase / AroAG


Mass: 10738.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: AROAG / Plasmid: pET 11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q72LN8, UniProt: Q5SLA5*PLUS, chorismate mutase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 1.79 Å3/Da / Density % sol: 31.36 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 6.2
Details: PEG 4K 27.5w/w(%), MES 0.1M, NaOH, Ca Chloride 0.01M, pH 6.2, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 23, 2005 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. all: 7950 / Num. obs: 7933 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 19.6
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 2.7 / Num. unique all: 685 / % possible all: 87.1

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2D8D

2d8d


Resolution: 1.75→28.84 Å / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 409 -RANDOM
Rwork0.225 ---
obs0.225 7524 93.1 %-
all-7933 --
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1-3.1 Å20 Å20 Å2
2---2.91 Å20 Å2
3----0.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.75→28.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms738 0 0 70 808
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d18.3
X-RAY DIFFRACTIONc_improper_angle_d1.01
LS refinement shellResolution: 1.75→1.81 Å / Rfactor Rfree error: 0.04
RfactorNum. reflection% reflection
Rfree0.253 40 -
Rwork0.284 --
obs-645 86.9 %

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