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- PDB-1vr6: Crystal structure of Phospho-2-dehydro-3-deoxyheptonate aldolase ... -

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Basic information

Entry
Database: PDB / ID: 1vr6
TitleCrystal structure of Phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthase) (TM0343) from Thermotoga Maritima at 1.92 A resolution
ComponentsPhospho-2-dehydro-3-deoxyheptonate aldolase
KeywordsTRANSFERASE / TM0343 / PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE (EC 2.5.1.54) (DAHP SYNTHASE) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
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
Phospho-2-dehydro-3-deoxyheptonate aldolase; domain 1 / 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 / Alpha-Beta Plaits / TIM Barrel ...Phospho-2-dehydro-3-deoxyheptonate aldolase; domain 1 / 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 / Alpha-Beta Plaits / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Phospho-2-dehydro-3-deoxyheptonate aldolase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Phospho-2-dehydro-3-deoxyheptonate aldolase (DAHP synthase) (TM0343) from Thermotoga Maritima at 1.92 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 14, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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
C: Phospho-2-dehydro-3-deoxyheptonate aldolase
D: Phospho-2-dehydro-3-deoxyheptonate aldolase


Theoretical massNumber of molelcules
Total (without water)155,5674
Polymers155,5674
Non-polymers00
Water11,079615
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14610 Å2
ΔGint-61 kcal/mol
Surface area46850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.151, 74.226, 249.540
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22B
32C
42D

NCS domain segments:

Component-ID: 1 / Refine code: 6

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISLYSLYSAA-4 - 708 - 82
21HISHISLYSLYSBB-3 - 709 - 82
31HISHISLYSLYSCC-4 - 708 - 82
41HISHISLYSLYSDD-2 - 7010 - 82
12LEULEUASNASNAA71 - 33883 - 350
22LEULEUASNASNBB71 - 33883 - 350
32LEULEUASNASNCC71 - 33883 - 350
42LEULEUASNASNDD71 - 33883 - 350

NCS ensembles :
ID
1
2

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Components

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


Mass: 38891.762 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0343 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WYH8, 3-deoxy-7-phosphoheptulonate synthase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 2.2 Å3/Da / Density % sol: 43.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 5.5
Details: 35.0% Ethylene-Glycol, 0.1M Acetate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2004 / Details: fixed-height exit beam, toroidal focusing mirror
RadiationMonochromator: Double-crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→47.76 Å / Num. obs: 102464 / % possible obs: 98.79 % / Redundancy: 3.57 % / Biso Wilson estimate: 44.73 Å2 / Rsym value: 0.065 / Net I/σ(I): 23.07
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 2.63 % / Mean I/σ(I) obs: 1.49 / Num. unique all: 4594 / Rsym value: 0.659 / % possible all: 90.38

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RZM

1rzm


Resolution: 1.92→47.76 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 7.386 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. THERE IS A LARGE POSITIVE PEAK BETWEEN RESIDUE 211 OF CHAINS A AND C AND B AND D.
RfactorNum. reflection% reflectionSelection details
Rfree0.21519 5111 5 %RANDOM
Rwork0.17089 ---
obs0.1732 97241 98.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.205 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.29 Å20 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.92→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10375 0 0 615 10990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02210573
X-RAY DIFFRACTIONr_bond_other_d0.0010.029954
X-RAY DIFFRACTIONr_angle_refined_deg1.5161.97914297
X-RAY DIFFRACTIONr_angle_other_deg0.842323062
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.94351353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.38923.858438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.676151853
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.191569
X-RAY DIFFRACTIONr_chiral_restr0.0930.21655
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211752
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022053
X-RAY DIFFRACTIONr_nbd_refined0.2130.22051
X-RAY DIFFRACTIONr_nbd_other0.1920.210028
X-RAY DIFFRACTIONr_nbtor_other0.0860.26179
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2591
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2980.268
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.218
X-RAY DIFFRACTIONr_mcbond_it2.11336915
X-RAY DIFFRACTIONr_mcbond_other0.60432786
X-RAY DIFFRACTIONr_mcangle_it3.095510835
X-RAY DIFFRACTIONr_scbond_it5.24784023
X-RAY DIFFRACTIONr_scangle_it7.058113462
X-RAY DIFFRACTIONr_nbtor_refined0.1720.25162
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1026loose positional0.625
12B1026loose positional0.625
13C1026loose positional0.665
14D1026loose positional0.675
11A1026loose thermal2.0510
12B1026loose thermal2.2210
13C1026loose thermal2.7310
14D1026loose thermal2.3910
21A3784loose positional0.495
22B3784loose positional0.535
23C3784loose positional0.495
24D3784loose positional0.485
21A3784loose thermal3.4810
22B3784loose thermal2.8410
23C3784loose thermal2.610
24D3784loose thermal2.5710
LS refinement shellResolution: 1.92→1.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 321 4.79 %
Rwork0.21 6387 -
obs--88.53 %
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)
17.27520.41462.13893.40761.75751.4194-0.0864-0.55580.08640.20510.0570.2715-0.0737-0.31040.0294-0.11220.0711-0.02680.07850.03750.0528-38.129-17.68838.319
21.9343-0.19850.63191.4756-0.3891.77150.0154-0.2259-0.01340.0176-0.0584-0.10580.0726-0.03810.043-0.27870.0049-0.0086-0.1489-0.0426-0.2117-1.651-30.88851.091
35.06412.5242-0.73746.3550.7951.791-0.08210.305-0.1858-0.73560.148-0.2934-0.3286-0.0731-0.0660.06810.00840.0743-0.1533-0.0455-0.0535-3.738-64.87524.034
41.33980.1374-0.46722.9019-0.48272.1186-0.10.26630.0787-0.63670.0396-0.09380.0433-0.11460.0604-0.0412-0.02610.0602-0.18170.0046-0.2064-0.446-24.68216.69
55.41161.8828-0.18023.6391-0.19481.70450.0495-0.3733-0.34090.04350.0483-0.2844-0.02620.0349-0.0977-0.11480.0190.0437-0.0468-0.0003-0.02774.859-58.85140.238
62.752-0.2207-0.50421.47180.10322.3699-0.0441-0.2089-0.06310.0171-0.01930.2766-0.046-0.29650.0634-0.2603-0.0320.0029-0.04170.0141-0.093-33.234-46.90447.374
74.3291.27070.93666.01541.18192.09940.05090.2680.4192-0.5847-0.03830.279-0.3094-0.1106-0.01260.00660.0606-0.0582-0.03590.05450.0746-26.859-9.83825.319
81.3216-0.16670.33192.70220.64573.0486-0.01470.2993-0.1375-0.6461-0.0550.16750.1886-0.12860.06970.0722-0.0549-0.1198-0.0489-0.0582-0.1207-28.124-49.51313.261
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA-4 - 708 - 82
22AA71 - 33883 - 350
33BB-3 - 709 - 82
44BB71 - 33883 - 350
55CC-4 - 708 - 82
66CC71 - 33883 - 350
77DD-2 - 7010 - 82
88DD71 - 33883 - 350

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