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- PDB-3toz: 2.2 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from ... -

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Basic information

Entry
Database: PDB / ID: 3toz
Title2.2 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with NAD.
ComponentsShikimate dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / NAD(P)-binding Rossmann-fold domain / Shikimate 5-dehydrogenase / NAD
Function / homology
Function and homology information


shikimate dehydrogenase (NADP+) / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NADP binding
Similarity search - Function
Shikimate 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 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...Shikimate 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 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Shikimate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMinasov, G. / Light, S.H. / Halavaty, A. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 2.2 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with NAD.
Authors: Minasov, G. / Light, S.H. / Halavaty, A. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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

Downloads & links

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Assembly

Deposited unit
A: Shikimate dehydrogenase
B: Shikimate dehydrogenase
C: Shikimate dehydrogenase
D: Shikimate dehydrogenase
E: Shikimate dehydrogenase
F: Shikimate dehydrogenase
G: Shikimate dehydrogenase
H: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,77728
Polymers279,5608
Non-polymers6,21820
Water18,1951010
1
A: Shikimate dehydrogenase
B: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6979
Polymers69,8902
Non-polymers1,8077
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6450 Å2
ΔGint-108 kcal/mol
Surface area24830 Å2
MethodPISA
2
C: Shikimate dehydrogenase
D: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,2886
Polymers69,8902
Non-polymers1,3984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-47 kcal/mol
Surface area24390 Å2
MethodPISA
3
E: Shikimate dehydrogenase
F: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3486
Polymers69,8902
Non-polymers1,4584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5560 Å2
ΔGint-54 kcal/mol
Surface area24580 Å2
MethodPISA
4
G: Shikimate dehydrogenase
H: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4447
Polymers69,8902
Non-polymers1,5545
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5880 Å2
ΔGint-65 kcal/mol
Surface area25090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.130, 78.434, 214.829
Angle α, β, γ (deg.)90.00, 90.49, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChain A and B, C and D, E and F, G and H represent Biological Assembly, dimer.

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Components

#1: Protein
Shikimate dehydrogenase


Mass: 34944.953 Da / Num. of mol.: 8 / Fragment: Shikimate 5-dehydrogenase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: aroE, lmo0490 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q8Y9N5, shikimate dehydrogenase (NADP+)
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1010 / 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: 2.11 Å3/Da / Density % sol: 41.8 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 7.5mG/mL, 0.25M Sodium chloride, 0.01M TRIS-HCl (pH 8.3); Screen: Classics II (F8), 0.2M Ammonium sulfate, 0.1M HEPES (pH 7.5), 25% (w/v) PEG R3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 14, 2011 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 117864 / Num. obs: 117864 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.5 / Num. unique all: 5755 / % possible all: 97.3

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1NPD

1npd


Resolution: 2.2→29.63 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.922 / SU B: 17.282 / SU ML: 0.198
Isotropic thermal model: Atomic Thermal Factors Individually Refined.
Cross valid method: THROUGHOUT / ESU R Free: 0.243 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25584 5836 5 %RANDOM
Rwork0.19547 ---
all0.19855 110577 --
obs0.19855 110577 98.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.413 Å2
Baniso -1Baniso -2Baniso -3
1--3.3 Å20 Å2-2.45 Å2
2--4.26 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17938 0 396 1010 19344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02218937
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212573
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9925700
X-RAY DIFFRACTIONr_angle_other_deg0.856330944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.27452361
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.15925.209791
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.635153392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.6261575
X-RAY DIFFRACTIONr_chiral_restr0.0890.22926
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0220821
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023554
X-RAY DIFFRACTIONr_mcbond_it0.971.511617
X-RAY DIFFRACTIONr_mcbond_other0.2971.54796
X-RAY DIFFRACTIONr_mcangle_it1.634218757
X-RAY DIFFRACTIONr_scbond_it2.95137320
X-RAY DIFFRACTIONr_scangle_it4.2814.56943
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 383 -
Rwork0.261 8015 -
obs-8015 97.28 %
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)
11.11380.05840.15250.56390.02182.31490.02160.37540.20140.09860.0009-0.1163-0.0047-0.0341-0.02250.13970.0308-0.02490.13880.05070.22085.8276-0.978273.0379
23.75850.2981-2.3173.0446-0.53432.459-0.02920.7342-0.1991-0.15820.013-0.03250.34750.0730.01610.19450.0835-0.02960.5116-0.03960.14114.493-6.889648.9604
33.3201-0.09-0.66470.64290.32821.80770.23730.42380.4977-0.04950.0523-0.1696-0.2350.0679-0.28960.14790.01820.01710.09770.10390.302113.32189.709360.1187
41.4145-0.229-0.11920.66070.2331.8207-0.0436-0.36150.1885-0.02230.06880.0263-0.025-0.109-0.02520.03570.0226-0.0280.1076-0.04930.0929.7999-1.396105.5911
54.7052-0.4532-0.55182.21090.82762.99790.0339-0.9967-0.26760.0906-0.09890.01460.51510.17650.06510.13870.1214-0.01330.51610.01560.02262.7982-5.8747128.7337
63.02840.1655-1.52850.49340.38362.90270.0833-0.51860.4571-0.0451-0.03090.0264-0.2619-0.0884-0.05240.12650.0767-0.0490.1902-0.14350.20083.393410.0458117.3326
72.1147-0.0608-0.40350.7096-0.35414.47040.1177-0.46730.071-0.1524-0.0245-0.1755-0.0093-0.0425-0.09320.2134-0.0202-0.0090.11160.01560.328224.2125-34.369785.4067
83.635-0.01730.27161.7055-0.63951.17670.0669-1.01560.12470.0753-0.0346-0.0204-0.0464-0.2036-0.03240.0291-0.048-0.01030.3475-0.01040.014330.8651-37.7393110.6278
97.22271.70780.87960.6666-0.15858.52820.2176-0.1359-0.7579-0.05020.0214-0.24881.0302-0.6235-0.2390.3094-0.0648-0.03250.05110.01030.249920.9189-45.658189.0894
102.06860.4231-0.70330.52090.24732.94560.10470.64780.10340.03710.03890.0443-0.0520.0416-0.14360.14580.04230.00810.2810.0460.232530.805-33.820957.5219
115.17160.00321.36581.51380.22332.1453-0.14822.00730.6253-0.29170.07710.0261-0.32580.61880.07110.1787-0.0555-0.02721.06180.24840.127623.318-31.367232.1457
124.35110.30962.75531.13840.18372.73510.23490.9396-0.55980.02590.0627-0.06750.39290.4578-0.29760.13380.089-0.0140.3797-0.12850.106826.8151-45.542146.2464
130.73370.2020.38230.5385-0.01832.31310.0409-0.16460.0347-0.00970.03790.0283-0.1073-0.2785-0.07880.07740.03340.02570.08380.01130.1403-26.81836.999655.2836
141.38710.2083-0.10951.5849-0.02380.11630.0778-0.5088-0.06930.1116-0.0294-0.09380.09680.0659-0.04850.1246-0.0032-0.03030.21370.0330.1349-18.655-5.422472.5729
156.3897-3.76654.16832.3388-2.14535.5720.37470.1849-0.5006-0.0271-0.21680.27610.6748-0.3744-0.15790.3631-0.1108-0.01560.22470.05430.1803-31.5692-5.700550.1431
160.81680.08920.49170.24770.06392.4990.0150.2091-0.1143-0.01590.07890.03330.0758-0.0466-0.09390.10370.02970.01670.09370.0010.1386-23.59019.282417.319
172.32760.23030.60081.5792-0.16911.6733-0.01230.1173-0.0921-0.17260.09670.07040.05320.0744-0.08440.05350.00780.00560.0886-0.03710.0478-32.65016.1376-2.4701
184.22440.1129-1.58845.5559-1.60731.3821-0.0293-0.1248-0.4854-0.3731-0.096-0.54660.2286-0.18810.12530.39580.0611-0.07670.4262-0.00210.3788-19.1515-3.45317.6716
191.95750.2632-0.05560.61920.05742.12530.0069-0.4697-0.03350.02640.07640.10360.03020.1494-0.08340.07610.0413-0.02420.16910.0150.0856-5.0605-36.504536.1063
203.14210.6232-1.32724.3252-0.27084.261-0.1368-1.3024-0.42440.1390.08380.0610.5880.47960.05290.20080.1098-0.04970.72440.18470.0972-7.4338-42.80261.473
213.2487-0.2476-2.13240.48120.10642.81180.1839-0.61450.35490.00910.0680.0875-0.29080.3713-0.25190.1039-0.0110.00440.2507-0.08380.1285-11.0442-26.259249.1435
220.6926-0.11060.20051.0716-0.07452.4981-0.02970.04010.0294-0.05560.145-0.09190.0495-0.0321-0.11530.0452-0.007-0.0330.0271-0.00190.0993-10.5802-36.10259.5282
232.32240.5951-0.00140.7773-0.20652.54510.050.3083-0.1169-0.08390.039-0.0180.1264-0.1045-0.0890.0816-0.0012-0.0210.0515-0.00220.0771-5.7029-32.7748-18.667
243.6884-0.49730.96282.9385-1.1024.6034-0.0875-0.03180.35810.01790.0465-0.0001-0.4931-0.02250.0410.0912-0.0031-0.04810.05060.03040.1167-14.9802-24.31782.9179
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 159
2X-RAY DIFFRACTION2A160 - 209
3X-RAY DIFFRACTION3A210 - 291
4X-RAY DIFFRACTION4B2 - 165
5X-RAY DIFFRACTION5B166 - 213
6X-RAY DIFFRACTION6B214 - 291
7X-RAY DIFFRACTION7C5 - 132
8X-RAY DIFFRACTION8C133 - 262
9X-RAY DIFFRACTION9C263 - 291
10X-RAY DIFFRACTION10D3 - 153
11X-RAY DIFFRACTION11D154 - 232
12X-RAY DIFFRACTION12D233 - 291
13X-RAY DIFFRACTION13E3 - 192
14X-RAY DIFFRACTION14E193 - 267
15X-RAY DIFFRACTION15E268 - 291
16X-RAY DIFFRACTION16F5 - 166
17X-RAY DIFFRACTION17F167 - 268
18X-RAY DIFFRACTION18F269 - 291
19X-RAY DIFFRACTION19G1 - 168
20X-RAY DIFFRACTION20G169 - 205
21X-RAY DIFFRACTION21G206 - 291
22X-RAY DIFFRACTION22H1 - 119
23X-RAY DIFFRACTION23H120 - 265
24X-RAY DIFFRACTION24H266 - 291

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