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- PDB-3pg8: Truncated form of 3-deoxy-D-arabino-heptulosonate 7-phosphate syn... -

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Basic information

Entry
Database: PDB / ID: 3pg8
TitleTruncated form of 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Thermotoga maritima
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase
KeywordsTRANSFERASE / Thermotoga maritima / DAH7PS / Shikimate pathway / aromatic biosynthesis / Tim barrel
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aldehyde-lyase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
DAHP synthase ferredoxin-like domain / DAHP synthase ferredoxin-like domain / Phospho-2-dehydro-3-deoxyheptonate aldolase, subtype 2 / : / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCross, P.J. / Dobson, R.C.J. / Patchett, M.L. / Parker, E.J.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Tyrosine latching of a regulatory gate affords allosteric control of aromatic amino acid biosynthesis
Authors: Cross, P.J. / Dobson, R.C.J. / Patchett, M.L. / Parker, E.J.
History
DepositionOct 31, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 22, 2012Group: Database references
Revision 1.3Nov 12, 2014Group: Other
Revision 1.4Nov 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phospho-2-dehydro-3-deoxyheptonate aldolase
B: Phospho-2-dehydro-3-deoxyheptonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4959
Polymers59,9012
Non-polymers5957
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-22 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.510, 55.456, 166.935
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phospho-2-dehydro-3-deoxyheptonate aldolase / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3- ...3-deoxy-D-arabino-heptulosonate 7-phosphate synthase / DAHP synthase / Phospho-2-keto-3-deoxyheptonate aldolase


Mass: 29950.326 Da / Num. of mol.: 2 / Fragment: Catalytic domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 (DSM3109) / Gene: aroF / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9WYH8, 3-deoxy-7-phosphoheptulonate synthase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.07 Å3/Da / Density % sol: 40.51 % / Mosaicity: 0.48 °
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 8%(w/v) PEG 4000, 0.1M sodium acetate, 0.02%(w/v) sodium azide, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→45.047 Å / Num. all: 32385 / Num. obs: 32385 / % possible obs: 94.5 % / Redundancy: 3.7 % / Biso Wilson estimate: 26.42 Å2 / Rsym value: 0.067 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2-2.113.70.3370.29321755847230.1620.3370.2934.196.3
2.11-2.243.70.2370.2063.61687045180.1130.2370.2065.596.3
2.24-2.393.70.1530.1335.41566141950.0740.1530.1337.995.4
2.39-2.583.80.1220.1065.71468139140.0590.1220.1069.895.1
2.58-2.833.70.0980.0853.51344936050.0470.0980.08512.294.7
2.83-3.163.70.0740.0646.91204032250.0360.0740.06415.593.9
3.16-3.653.70.0680.05910.11060128710.0340.0680.05919.793.7
3.65-4.473.70.0610.05311.1881024080.030.0610.0532392.2
4.47-6.323.50.0450.03914.4656318730.0230.0450.03925.691.3
6.32-45.0473.70.0440.03813.6391410530.0210.0440.03828.888.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data processing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RZM

1rzm


Resolution: 2→38.57 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.8828 / SU ML: 0.23 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 2006 6.2 %Random
Rwork0.1546 ---
obs0.158 32352 93.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.075 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 118.59 Å2 / Biso mean: 30.2709 Å2 / Biso min: 10.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.0436 Å20 Å2-0 Å2
2--1.3396 Å20 Å2
3----0.296 Å2
Refinement stepCycle: LAST / Resolution: 2→38.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3940 0 39 238 4217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064121
X-RAY DIFFRACTIONf_angle_d0.9955580
X-RAY DIFFRACTIONf_chiral_restr0.07645
X-RAY DIFFRACTIONf_plane_restr0.004723
X-RAY DIFFRACTIONf_dihedral_angle_d13.4671506
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.07150.23852040.17093040324496
2.0715-2.15450.23221940.15583059325396
2.1545-2.25250.22211970.15793042323996
2.2525-2.37120.21591980.14733029322795
2.3712-2.51980.20291990.14653032323194
2.5198-2.71430.22222020.15733031323395
2.7143-2.98730.2262040.15663022322694
2.9873-3.41940.19912020.14873013321593
3.4194-4.30720.19252020.13833021322392
4.3072-38.57710.20142040.16493057326189
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)
11.2197-1.1646-0.03291.12760.20531.4017-0.1143-0.02480.1650.03990.0382-0.052-0.1346-0.02760.07590.1724-0.0137-0.04790.12240.00370.194610.5222-2.2074-32.0909
20.7771-0.53380.31671.82990.31691.2255-0.01080.0709-0.0707-0.09-0.06790.22870.0231-0.17910.06680.1340.0027-0.04190.11990.00140.15912.633-7.9151-36.7681
31.0542-0.4370.56791.02580.22331.01340.0143-0.1419-0.11820.0790.0290.04040.1025-0.0707-0.05030.1732-0.0232-0.040.16890.01930.182411.9222-20.3395-32.3871
41.1531-0.23440.75931.4616-0.10630.5013-0.1661-0.28870.09950.25590.13690.1721-0.0362-0.1530.02960.19970.031-0.01040.18710.0150.183214.4099-9.738-19.7934
51.3256-0.05120.86972.26221.37087.2031-0.044-0.30560.30090.28730.0828-0.1994-0.4869-0.25620.18370.16170.0106-0.09970.08470.01160.182118.7621-3.6362-19.5849
60.7313-0.5076-0.8292.13240.01781.1419-0.1436-0.44730.31640.71260.0750.5892-0.21140.02930.00340.2238-0.02580.04830.2166-0.02580.243918.8535-21.60713.7002
71.1553-0.5315-0.18821.0605-0.49971.4729-0.0425-0.0785-0.1026-0.0643-0.043-0.09190.22170.28630.04990.12130.0102-0.0030.20140.02240.172540.9534-33.9129-12.5911
80.8335-0.5597-0.14660.5963-0.32061.113-0.0535-0.0623-0.1384-0.00630.02940.10920.02-0.0540.02960.1494-0.0115-0.01220.15060.03170.158928.4554-42.077-3.9816
91.1007-0.13360.07530.8237-0.70980.99850.02570.047-0.0129-0.0528-0.01080.11770.1325-0.0791-0.05180.1552-0.0102-0.01310.15350.01150.127522.3786-27.8902-12.9377
101.8158-0.601-0.68480.9707-0.00941.92010.22460.3994-0.0005-0.1617-0.2606-0.2650.01480.02770.04860.17460.0027-0.01110.22010.01060.165536.7158-26.7369-23.3932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 68:156)A68 - 156
2X-RAY DIFFRACTION2(chain A and resid 157:209)A157 - 209
3X-RAY DIFFRACTION3(chain A and resid 210:266)A210 - 266
4X-RAY DIFFRACTION4(chain A and resid 267:304)A267 - 304
5X-RAY DIFFRACTION5(chain A and resid 305:338)A305 - 338
6X-RAY DIFFRACTION6(chain B and resid 68:79)B68 - 79
7X-RAY DIFFRACTION7(chain B and resid 80:163)B80 - 163
8X-RAY DIFFRACTION8(chain B and resid 164:201)B164 - 201
9X-RAY DIFFRACTION9(chain B and resid 202:296)B202 - 296
10X-RAY DIFFRACTION10(chain B and resid 297:338)B297 - 338

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