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- PDB-3tnl: 1.45 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 3tnl
Title1.45 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with Shikimate and 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 / Chem-SKM / Shikimate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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: 1.45 Angstrom Crystal Structure of Shikimate 5-dehydrogenase from Listeria monocytogenes in Complex with Shikimate and 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 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,92414
Polymers139,7804
Non-polymers3,14410
Water34,3551907
1
A: Shikimate dehydrogenase
B: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4627
Polymers69,8902
Non-polymers1,5725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6330 Å2
ΔGint-46 kcal/mol
Surface area24340 Å2
MethodPISA
2
C: Shikimate dehydrogenase
D: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4627
Polymers69,8902
Non-polymers1,5725
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-44 kcal/mol
Surface area24500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.851, 82.878, 101.260
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChain A and B, C and D form dimers

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Components

#1: Protein
Shikimate dehydrogenase


Mass: 34944.953 Da / Num. of mol.: 4
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.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-SKM / (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID / SHIKIMATE


Mass: 174.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H10O5
#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.: 1907 / 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: 2.16 Å3/Da / Density % sol: 42.97 %
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), 1mM Shikimate; Screen: PEG's (D2), 0.1M HEPES (pH 7.5), 25% (w/v) PEG 4000. , VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 24, 2011 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 203043 / Num. obs: 203043 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 20.6
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.1 / Num. unique all: 9339 / % possible all: 89.4

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
BALBESphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1NPD

1npd


Resolution: 1.45→29.31 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.349 / SU ML: 0.042
Isotropic thermal model: Atomic Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17645 10155 5 %RANDOM
Rwork0.14871 ---
all0.15011 192681 --
obs0.15011 192681 96.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.508 Å2
Baniso -1Baniso -2Baniso -3
1--1.26 Å2-0 Å21.23 Å2
2--1.72 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8944 0 204 1907 11055
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0229814
X-RAY DIFFRACTIONr_bond_other_d0.0010.026537
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.99413361
X-RAY DIFFRACTIONr_angle_other_deg0.898316121
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.87251248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.38525.306409
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.119151779
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3251539
X-RAY DIFFRACTIONr_chiral_restr0.10.21514
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210969
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021852
X-RAY DIFFRACTIONr_mcbond_it1.0791.56022
X-RAY DIFFRACTIONr_mcbond_other0.3821.52474
X-RAY DIFFRACTIONr_mcangle_it1.76129773
X-RAY DIFFRACTIONr_scbond_it2.92233792
X-RAY DIFFRACTIONr_scangle_it4.7084.53588
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.259 673 -
Rwork0.237 13240 -
obs-13240 90.3 %
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)
10.1349-0.0067-0.08990.14530.04760.4360.0139-0.00910.006-0.0059-0.00030.00950.005-0.0075-0.01360.0430.0060.01740.00230.0020.06334.299337.570374.7144
20.45320.02960.17790.05210.01370.546-0.00020.03530.0180.0145-0.0096-0.0064-0.00610.00180.00980.03690.0040.02170.0089-0.00230.052826.88136.844548.0168
30.55960.6037-0.22090.55560.06970.6592-0.00510.0502-0.0218-0.0020.0329-0.05150.07920.0244-0.02780.05950.01490.00830.004-0.0110.069839.622825.687166.5648
40.0704-0.0377-0.13820.0173-0.0090.89260.0144-0.0480.0124-0.0170.0216-0.02150.022-0.0313-0.03610.033-0.0130.01910.03280.00220.047329.00635.284293.4297
50.3508-0.08840.00850.0887-0.09390.42940.0107-0.00940.012-0.00970.0071-0.0320.002-0.0763-0.01770.03790.00020.0250.0222-0.00110.046235.267929.8413120.3258
60.1452-0.6725-0.26270.75250.2940.9104-0.0092-0.04280.04520.04120.03610.01390.2172-0.1123-0.02690.0838-0.03630.00660.02390.01860.035125.553121.81798.365
70.12070.0370.04490.0423-0.01090.65560.01260.0078-0.01570.00380.00760.00820.00750.0639-0.02020.03610.00150.01820.0041-0.00450.0714-7.205729.940924.2127
80.5210.0093-0.21820.0223-0.02290.43170.00650.0639-0.04020.0287-0.03090.0068-0.0062-0.01350.02440.0365-0.00630.01780.0221-0.00870.05580.086730.5299-2.5487
90.52491.0097-0.04231.5409-0.45461.297-0.01540.0648-0.01880.06190.04610.0282-0.1650.0239-0.03070.0648-0.00820.03350.00110.0050.0681-12.483241.859816.0295
100.1812-0.040.14370.024-0.0490.76340.0122-0.0507-0.0231-0.01190.03570.0578-0.01890.107-0.04790.0265-0.01460.01590.03850.00850.0642-2.175831.677342.4467
110.4204-0.0242-0.03220.00740.04370.6580.0153-0.04260.0077-0.01860.01520.0411-0.00790.1196-0.03050.0236-0.00090.01620.0451-0.01120.0454-8.143737.637169.2965
120.7681-0.85990.06381.1284-0.08380.66330.0304-0.10260.0006-0.0010.03780.006-0.17460.1878-0.06820.0575-0.05540.03730.0603-0.02630.03351.651845.781447.634
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 112
2X-RAY DIFFRACTION2A113 - 268
3X-RAY DIFFRACTION3A269 - 291
4X-RAY DIFFRACTION4B3 - 117
5X-RAY DIFFRACTION5B118 - 267
6X-RAY DIFFRACTION6B268 - 291
7X-RAY DIFFRACTION7C3 - 112
8X-RAY DIFFRACTION8C113 - 269
9X-RAY DIFFRACTION9C270 - 291
10X-RAY DIFFRACTION10D4 - 113
11X-RAY DIFFRACTION11D114 - 268
12X-RAY DIFFRACTION12D269 - 291

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