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- PDB-3nud: The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synt... -

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Basic information

Entry
Database: PDB / ID: 3nud
TitleThe structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from mycobacterium tuberculosis complexed with phenylalanine
ComponentsProbable 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase AroG
KeywordsTRANSFERASE / Mycobacterium tuberculosis / DAH7P synthase / Shikimate pathway / Aromatic biosynthesis / Evolutionary relationships / Phe-bound / Augmented TIM-barrel structure
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 / Phospho-2-dehydro-3-deoxyheptonate aldolase AroG
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsParker, E.J. / Jameson, G.B. / Jiao, W. / Webby, C.J. / Baker, E.N. / Baker, H.M.
CitationJournal: 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.
History
DepositionJul 6, 2010Deposition 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)102,95812
Polymers101,6572
Non-polymers1,30110
Water18010
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)205,91524
Polymers203,3144
Non-polymers2,60220
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area11680 Å2
ΔGint-88 kcal/mol
Surface area63270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.650, 204.650, 66.610
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
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A3 - 10
2116B1 - 10
1212A20 - 190
2212B20 - 190
1312A205 - 232
2312B205 - 232
1412A243 - 261
2412B243 - 261
1512A271 - 367
2512B271 - 367
1612A386 - 411
2612B386 - 411
1712A448 - 462
2712B448 - 462
1126A11 - 19
2126B11 - 19
1226A191 - 204
2226B191 - 204
1326A233 - 241
2326B233 - 241
1426A262 - 270
2426B262 - 270
1526A368 - 385
2526B368 - 385
1626A412 - 447
2626B412 - 447

NCS ensembles :
ID
1
2

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Components

#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 (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O53512, 3-deoxy-7-phosphoheptulonate synthase
#2: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H11NO2
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.96 Å3/Da / Density % sol: 68.95 %
Crystal growTemperature: 295 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 295K

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Data collection

DiffractionMean temperature: 123 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 24, 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: 3→39.6 Å / Num. all: 31363 / Num. obs: 31363 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.63 % / Biso Wilson estimate: 36.2 Å2 / Rmerge(I) obs: 0.164 / Net I/σ(I): 5.6
Reflection shellResolution: 3→3.077 Å / Redundancy: 2.68 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 3 / Num. unique all: 31363 / % possible all: 97.2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CCP4model building
REFMAC5.5.0072refinement
d*TREKdata reduction
d*TREKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2B7O

2b7o


Resolution: 3→39.55 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.824 / SU B: 36.052 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.375 / ESU R Free: 0.405 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2694 1574 5.1 %RANDOM
Rwork0.21227 ---
obs0.21517 29566 96.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.676 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20.32 Å20 Å2
2--0.63 Å20 Å2
3----0.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.405 Å1.375 Å
Refinement stepCycle: LAST / Resolution: 3→39.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6756 0 85 10 6851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0217121
X-RAY DIFFRACTIONr_bond_other_d0.0010.024745
X-RAY DIFFRACTIONr_angle_refined_deg1.161.969695
X-RAY DIFFRACTIONr_angle_other_deg1.27311511
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4885897
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.46923.313329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.952151115
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2041566
X-RAY DIFFRACTIONr_chiral_restr0.0710.21098
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218026
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021435
X-RAY DIFFRACTIONr_mcbond_it1.3331.54527
X-RAY DIFFRACTIONr_mcbond_other0.1881.51810
X-RAY DIFFRACTIONr_mcangle_it2.44727262
X-RAY DIFFRACTIONr_scbond_it3.12432594
X-RAY DIFFRACTIONr_scangle_it5.1434.52433
Refine LS restraints NCS

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

Ens-IDNumberTypeRms dev position (Å)Weight position
12079tight positional0.250.3
12499medium positional0.431
178loose positional5.762
2926loose positional0.782
12079tight thermal1.552.5
12499medium thermal1.742
178loose thermal1.1910
2926loose thermal3.9510
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 116 -
Rwork0.296 2171 -
obs-2171 96.87 %
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)
10.6237-0.133-0.12880.37090.1020.24610.0236-0.04560.06980.0111-0.0061-0.0659-0.02320.0157-0.01750.01580.0069-0.00950.0137-0.01030.022438.2232114.898515.5658
20.3481-0.21950.10790.3780.0020.1153-0.0021-0.0405-0.05710.02560.00960.0592-0.0212-0.0293-0.00750.01440.00410.00170.0090.00420.011819.986490.3889-6.7923
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 462
2X-RAY DIFFRACTION2B1 - 462

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