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- PDB-3kgf: The structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synt... -

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Basic information

Entry
Database: PDB / ID: 3kgf
TitleThe structure of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis complexed with phenylalanine and tryptophan
ComponentsProbable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
KeywordsTRANSFERASE / Mycobacterium tuberculosis / DAH7P synthase / Shikimate pathway / Aromatic biosynthesis / Evolutionary relationships / PHE+TRP-bound / Augmented TIM-barrel structure / Structural Genomics / Mycobacterium Tuberculosis Structural Proteomics Project / XMTB
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / peptidoglycan-based cell wall / protein homooligomerization / manganese ion binding / plasma membrane / cytosol
Similarity search - Function
DAHP synthetase, class II / Class-II DAHP synthetase family / Aldolase-type TIM barrel
Similarity search - Domain/homology
: / PHENYLALANINE / PHOSPHATE ION / TRYPTOPHAN / Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsParker, E.J. / Jameson, G.B. / Jiao, W. / Webby, C.J. / Baker, E.N. / Baker, H.M. / Mycobacterium Tuberculosis Structural Proteomics Project (XMTB)
Citation
Journal: J.Biol.Chem. / Year: 2010
Title: Synergistic allostery, a sophisticated regulatory network for the control of aromatic amino acid biosynthesis in Mycobacterium tuberculosis
Authors: Webby, C.J. / Jiao, W. / Hutton, R.D. / Blackmore, N.J. / Baker, H.M. / Baker, E.N. / Jameson, G.B. / Parker, E.J.
#1: Journal: J.Mol.Biol. / Year: 2005
Title: The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for type I and type II enzymes
Authors: Webby, C.J. / Baker, H.M. / Lott, J.S. / Baker, E.N. / Parker, E.J.
#2: Journal: Biochemistry / Year: 2005
Title: Substrate ambiguity and crystal structure of Pyrococcus furiosus 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase: an ancestral 3-deoxyald-2-ulosonate-phosphate synthase?
Authors: Schofield, L.R. / Anderson, B.F. / Patchett, M.L. / Norris, G.E. / Jameson, G.B. / Parker, E.J.
History
DepositionOct 29, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Database references
Revision 1.3Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
B: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,69232
Polymers101,6572
Non-polymers3,03530
Water13,890771
1
A: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
B: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
hetero molecules

A: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
B: Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)209,38464
Polymers203,3144
Non-polymers6,07160
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area12290 Å2
ΔGint-80 kcal/mol
Surface area62020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.537, 204.537, 66.462
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: 5

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1ASNASNAA2 - 4624 - 464
2METMETBB1 - 4623 - 464

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Probable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG / DAHP synthetase / phenylalanine-repressible


Mass: 50828.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv2178c / Plasmid: PproExHTa / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O53512, 3-deoxy-7-phosphoheptulonate synthase

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Non-polymers , 8 types, 801 molecules

#2: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 771 / 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: 3.95 Å3/Da / Density % sol: 68.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20mM BTP, 150mM NaCl, 0.5mM TCEP, 0.005%(v/v) Thesit, 0.2mM PEP, 0.1mM MnCl2, 0.1M Na HEPES, 0.8M NaK phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 14, 2005 / Details: Osmic Blue Mirrors
RadiationMonochromator: OSMIC BLUE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2→39.5 Å / Num. all: 105425 / Num. obs: 105425 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.07 % / Biso Wilson estimate: 37.5 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 8.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.38 % / Rmerge(I) obs: 0.381 / Mean I/σ(I) obs: 2.1 / Num. unique all: 10487 / % possible all: 87.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CCP4model building
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2b7o

2b7o


Resolution: 2→32.67 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 5.535 / SU ML: 0.082 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MN is chain A is present in 75% occupancy, while in chain B its occupancy is 50%. The water that is observed coordinated to the MN ion in ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. MN is chain A is present in 75% occupancy, while in chain B its occupancy is 50%. The water that is observed coordinated to the MN ion in chain A is displaced to more than 4 Angstroms away from the MN in chain B. Atom OE1 of GLU411 is weakly coordinated at distances greater than 2.6 Angstroms for both MN sites. Because the occupancy of MN in chain B is only two-thirds that of the MN in chain A, MN-ligand distances in chain B are ~0.2 A longer than the corresponding distances in chain A.
RfactorNum. reflection% reflectionSelection details
Rfree0.191 5245 5 %RANDOM
Rwork0.163 99865 --
all0.16423 105110 --
obs0.164 105110 97.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.1 Å2 / Biso mean: 25.418 Å2 / Biso min: 9.29 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.08 Å20 Å2
2---0.15 Å20 Å2
3---0.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.112 Å0.118 Å
Refinement stepCycle: LAST / Resolution: 2→32.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6976 0 191 771 7938
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217699
X-RAY DIFFRACTIONr_bond_other_d0.0040.025214
X-RAY DIFFRACTIONr_angle_refined_deg1.3181.96710484
X-RAY DIFFRACTIONr_angle_other_deg0.976312647
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1875977
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.00323.261368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.893151225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7491579
X-RAY DIFFRACTIONr_chiral_restr0.0740.21155
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028748
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021568
X-RAY DIFFRACTIONr_nbd_refined0.2040.21536
X-RAY DIFFRACTIONr_nbd_other0.2030.25733
X-RAY DIFFRACTIONr_nbtor_refined0.1640.23665
X-RAY DIFFRACTIONr_nbtor_other0.0830.23753
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1630.2620
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1010.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2690.271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.231
X-RAY DIFFRACTIONr_mcbond_it0.6961.54950
X-RAY DIFFRACTIONr_mcbond_other0.1611.51917
X-RAY DIFFRACTIONr_mcangle_it1.0927751
X-RAY DIFFRACTIONr_scbond_it2.79653072
X-RAY DIFFRACTIONr_scangle_it4.2127.52731
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
2573MEDIUM POSITIONAL0.790.5
3018LOOSE POSITIONAL0.95
2573MEDIUM THERMAL0.622
3018LOOSE THERMAL1.3710
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 336 -
Rwork0.26 6339 -
all-6675 -
obs--84.82 %
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)
10.7881-0.2637-0.30040.76470.23490.65050.0491-0.12470.14570.09440.0291-0.1371-0.07950.0881-0.07820.01850.0236-0.00410.0021-0.0341-0.13438.274115.72714.975
20.8803-0.39740.16870.8191-0.05110.5050.048-0.0098-0.1695-0.0264-0.00960.1540.0192-0.0853-0.0385-0.05680.0271-0.0154-0.0033-0.0036-0.156619.79889.944-6.438
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 462
2X-RAY DIFFRACTION2B1 - 462

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