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- PDB-1nyt: SHIKIMATE DEHYDROGENASE AroE COMPLEXED WITH NADP+ -

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Basic information

Entry
Database: PDB / ID: 1nyt
TitleSHIKIMATE DEHYDROGENASE AroE COMPLEXED WITH NADP+
ComponentsShikimate 5-dehydrogenase
KeywordsOXIDOREDUCTASE / alpha/beta domains / wide cleft separation
Function / homology
Function and homology information


chorismate biosynthetic process => GO:0009423 / shikimate dehydrogenase (NADP+) / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / NADP binding / nucleotide binding / cytosol
Similarity search - Function
Shikimate dehydrogenase / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / Shikimate dehydrogenase family / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / NAD(P)-binding Rossmann-like Domain ...Shikimate dehydrogenase / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-dehydrogenase / Shikimate dehydrogenase family / SDH, C-terminal / Shikimate 5'-dehydrogenase C-terminal domain / Shikimate dehydrogenase substrate binding, N-terminal / Shikimate dehydrogenase substrate binding domain / Leucine Dehydrogenase, chain A, domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
(2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Shikimate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.5 Å
AuthorsRoszak, A.W. / Lapthorn, A.J.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Structures of shikimate dehydrogenase AroE and its Paralog YdiB. A common structural framework for different activities.
Authors: Michel, G. / Roszak, A.W. / Sauve, V. / Maclean, J. / Matte, A. / Coggins, J.R. / Cygler, M. / Lapthorn, A.J.
History
DepositionFeb 13, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Shikimate 5-dehydrogenase
B: Shikimate 5-dehydrogenase
C: Shikimate 5-dehydrogenase
D: Shikimate 5-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,95923
Polymers117,4864
Non-polymers4,47319
Water24,0141333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13650 Å2
ΔGint-237 kcal/mol
Surface area41820 Å2
MethodPISA
2
A: Shikimate 5-dehydrogenase
B: Shikimate 5-dehydrogenase
C: Shikimate 5-dehydrogenase
D: Shikimate 5-dehydrogenase
hetero molecules

A: Shikimate 5-dehydrogenase
B: Shikimate 5-dehydrogenase
C: Shikimate 5-dehydrogenase
D: Shikimate 5-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,91746
Polymers234,9728
Non-polymers8,94638
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area31090 Å2
ΔGint-498 kcal/mol
Surface area79840 Å2
MethodPISA
3
A: Shikimate 5-dehydrogenase
C: Shikimate 5-dehydrogenase
hetero molecules

A: Shikimate 5-dehydrogenase
C: Shikimate 5-dehydrogenase
hetero molecules

B: Shikimate 5-dehydrogenase
D: Shikimate 5-dehydrogenase
hetero molecules

B: Shikimate 5-dehydrogenase
D: Shikimate 5-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,91746
Polymers234,9728
Non-polymers8,94638
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
crystal symmetry operation3_545x+1/2,y-1/2,z1
crystal symmetry operation4_646-x+3/2,y-1/2,-z+11
Buried area33740 Å2
ΔGint-480 kcal/mol
Surface area77190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.524, 140.019, 102.712
Angle α, β, γ (deg.)90.00, 122.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1425-

HOH

21A-1426-

HOH

31A-1427-

HOH

41B-1436-

HOH

51B-1437-

HOH

61D-1687-

HOH

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Components

#1: Protein
Shikimate 5-dehydrogenase


Mass: 29371.490 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: AROE / Plasmid: pTB361 / Production host: Escherichia coli (E. coli) / Strain (production host): AB2834
References: UniProt: P15770, shikimate dehydrogenase (NADP+)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4 / Details: T7 RNA polymerase
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1333 / 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: 2.42 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.7
Details: 1.6M ammonium sulfate, 100mM cacodylate buffer, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2000 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.5→38.92 Å / Num. all: 210686 / Num. obs: 196162 / % possible obs: 93.11 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 18.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.766 / Mean I/σ(I) obs: 1.56 / Num. unique all: 9101 / % possible all: 86.7

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Processing

Software
NameVersionClassification
REFMAC5.1.27refinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(TRUNCATE)data scaling
MLPHAREphasing
SHELXDphasing
DMphasing
SOLVEphasing
RefinementMethod to determine structure: SIRAS / Resolution: 1.5→38.92 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.119 / SU ML: 0.041 / Isotropic thermal model: Anisotropic temperature factors / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16869 19515 9.9 %RANDOM
Rwork0.1323 ---
all0.13594 196162 --
obs0.13594 196162 93.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å2-0.01 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.064 Å0.071 Å
Refinement stepCycle: LAST / Resolution: 1.5→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8236 0 270 1333 9839
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0218760
X-RAY DIFFRACTIONr_bond_other_d0.0020.027916
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.99711925
X-RAY DIFFRACTIONr_angle_other_deg2.063318416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.53851077
X-RAY DIFFRACTIONr_chiral_restr0.1370.21334
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.029631
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021701
X-RAY DIFFRACTIONr_nbd_refined0.2250.21692
X-RAY DIFFRACTIONr_nbd_other0.250.29175
X-RAY DIFFRACTIONr_nbtor_other0.1060.24957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.2879
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.229
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3380.2125
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.260
X-RAY DIFFRACTIONr_mcbond_it1.7471.55353
X-RAY DIFFRACTIONr_mcangle_it2.54728577
X-RAY DIFFRACTIONr_scbond_it4.03233407
X-RAY DIFFRACTIONr_scangle_it5.7414.53348
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.287 1068
Rwork0.226 10088
obs-10088
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)
10.649-0.0105-0.1290.3037-0.00860.61-0.01080.0211-0.08110.0075-0.030.0054-0.0298-0.02820.04070.04760.0363-0.01370.0796-0.0050.06366.343424.396427.1614
20.65040.0902-0.21740.2889-0.05211.1529-0.0550.07330.02910.03720.05080.04170.067-0.09180.00410.04780.0173-0.01290.07960.00820.061948.692931.317914.1505
30.5660.250.02920.51640.28070.4970.03390.01020.0570.079-0.07890.04410.07780.03530.0450.07190.02410.01880.06570.00470.051343.527387.406126.915
40.56210.07770.04040.34180.07270.8278-0.04660.0711-0.0210.06590.0452-0.0656-0.01670.04250.00140.05390.02210.00110.0638-0.00450.076561.497780.789714.2255
50.4847-0.0297-0.09581.414-0.30920.9141-0.00810.07110.05240.061-0.05060.0151-0.09570.0640.05870.04660.0266-0.01340.05550.03470.075969.975953.219225.0478
61.2698-0.42580.1080.3778-0.02620.89540.06350.08290.1960.0208-0.0459-0.1566-0.07460.0361-0.01760.0439-0.0076-0.00190.04030.00630.123492.785644.215226.6419
70.871-0.27240.39210.9423-0.21530.65450.00790.0569-0.1108-0.003-0.02240.03450.0359-0.01110.01450.05270.04410.02450.0603-0.01870.077339.981458.880524.8604
81.1206-0.0422-0.18640.63220.16620.8680.02690.1019-0.01570.068-0.08230.08320.12-0.0620.05540.0538-0.00350.0180.0503-0.01510.080217.784467.541127.0539
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1011 - 101
2X-RAY DIFFRACTION1AA242 - 271242 - 271
3X-RAY DIFFRACTION1AG - T1404 - 14051
4X-RAY DIFFRACTION2AA102 - 241102 - 241
5X-RAY DIFFRACTION2AR - F1401 - 14031
6X-RAY DIFFRACTION3BB1 - 1011 - 101
7X-RAY DIFFRACTION3BB242 - 271242 - 271
8X-RAY DIFFRACTION3BJ - R1414 - 14341
9X-RAY DIFFRACTION4BB102 - 241102 - 241
10X-RAY DIFFRACTION4BU - I1411 - 14131
11X-RAY DIFFRACTION5CC1 - 1011 - 101
12X-RAY DIFFRACTION5CC242 - 269242 - 269
13X-RAY DIFFRACTION5CL - O1423 - 14261
14X-RAY DIFFRACTION6CC102 - 241102 - 241
15X-RAY DIFFRACTION6CV - K1421 - 14221
16X-RAY DIFFRACTION7DD1 - 1011 - 101
17X-RAY DIFFRACTION7DD242 - 270242 - 270
18X-RAY DIFFRACTION7DQ14331
19X-RAY DIFFRACTION8DD102 - 241102 - 241
20X-RAY DIFFRACTION8DW - P1431 - 14321

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