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- PDB-3t4e: 1.95 Angstrom Crystal Structure of Shikimate 5-dehydrogenase (Aro... -

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Basic information

Entry
Database: PDB / ID: 3t4e
Title1.95 Angstrom Crystal Structure of Shikimate 5-dehydrogenase (AroE) from Salmonella enterica subsp. enterica serovar Typhimurium in Complex with NAD
ComponentsQuinate/shikimate dehydrogenase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / NAD(P)-binding Rossmann-fold C-terminal domain / Aminoacid dehydrogenase-like N-terminal domain / NAD
Function / homology
Function and homology information


quinate/shikimate dehydrogenase [NAD(P)+] / quinate 3-dehydrogenase (NADP+) activity / quinate 3-dehydrogenase (NAD+) activity / shikimate 3-dehydrogenase (NAD+) activity / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process
Similarity search - Function
Quinate/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 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...Quinate/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 / 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 / PHOSPHATE ION / Quinate/shikimate dehydrogenase
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsMinasov, G. / Light, S.H. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.95 Angstrom Crystal Structure of Shikimate 5-dehydrogenase (AroE) from Salmonella enterica subsp. enterica serovar Typhimurium in Complex with NAD.
Authors: Minasov, G. / Light, S.H. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJul 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 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: Quinate/shikimate dehydrogenase
B: Quinate/shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7436
Polymers68,2262
Non-polymers1,5174
Water10,485582
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4630 Å2
ΔGint-46 kcal/mol
Surface area23930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.049, 111.392, 66.380
Angle α, β, γ (deg.)90.00, 96.20, 90.00
Int Tables number4
Space group name H-MP1211
DetailsChains A and B represent biological assembly

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Components

#1: Protein Quinate/shikimate dehydrogenase / NAD-dependent shikimate 5-dehydrogenase 2


Mass: 34112.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: LT2 / Gene: aroE, STM1359, ydiB / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic
References: UniProt: Q8ZPR4, quinate/shikimate dehydrogenase [NAD(P)+]
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 582 / 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: 42.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: Protein solution: 7.5 mG/mL, 0.25M Sodium chloride. 0.01M Tris HCl pH 8.3, Screen solution: PEG's (H3), 0.2M Sodium phosphate, 20% (w/v) PEG 3350, 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: 1.95→30 Å / Num. all: 39301 / Num. obs: 39301 / % possible obs: 93.6 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 17.7
Reflection shellResolution: 1.95→1.98 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.501 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2035 / % possible all: 97

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O9B

1o9b


Resolution: 1.95→28.39 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.09 / SU ML: 0.104
Isotropic thermal model: Atomic Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22006 1988 5.1 %RANDOM
Rwork0.16559 ---
all0.16831 37240 --
obs0.16831 37240 93.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.163 Å2
Baniso -1Baniso -2Baniso -3
1-1.06 Å2-0 Å20.65 Å2
2---0.83 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.95→28.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4321 0 98 582 5001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224670
X-RAY DIFFRACTIONr_bond_other_d0.0010.023088
X-RAY DIFFRACTIONr_angle_refined_deg1.491.9976350
X-RAY DIFFRACTIONr_angle_other_deg0.84437597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8925596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.09925.285193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.44115812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4781518
X-RAY DIFFRACTIONr_chiral_restr0.0810.2713
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025225
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02897
X-RAY DIFFRACTIONr_mcbond_it1.0321.52900
X-RAY DIFFRACTIONr_mcbond_other0.341.51199
X-RAY DIFFRACTIONr_mcangle_it1.76224656
X-RAY DIFFRACTIONr_scbond_it3.05831770
X-RAY DIFFRACTIONr_scangle_it4.7454.51694
LS refinement shellResolution: 1.952→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 168 -
Rwork0.185 2807 -
obs-2807 95.54 %
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)
13.0126-0.479-0.3121.81340.1270.93460.0125-0.10460.07910.1307-0.0003-0.118-0.03290.0842-0.01230.0634-0.0021-0.01660.0771-0.01270.06436.639846.361316.1697
20.6579-0.2423-0.22541.86380.57380.88020.00820.1082-0.0177-0.0811-0.0330.0453-0.01240.0060.02480.04740.0035-0.01140.11610.00020.07792.037537.28275.0112
31.4397-0.13070.26911.29760.03251.92170.0244-0.0233-0.15030.0677-0.01210.00190.2352-0.0047-0.01230.07640.0042-0.00250.067-0.00860.08983.286416.687910.8815
40.11670.3068-0.06262.3990.35460.35430.01310.0544-0.0860.0556-0.0263-0.26340.02540.06780.01320.0960.0161-0.00480.2112-0.01170.236817.025533.77019.1486
53.55050.68332.05654.23280.94474.68280.14440.1203-0.14570.2510.2066-0.77010.13510.307-0.3510.08830.0127-0.04580.089-0.08760.240910.853861.412819.8821
60.60240.13060.01243.57931.85520.99110.0039-0.03090.00660.4553-0.0750.17720.1853-0.02780.07110.1788-0.01230.03840.1107-0.01050.0914-2.710266.475124.5233
71.39540.3298-0.8251.41310.40783.30610.07440.04220.171-0.08230.0857-0.1033-0.31550.2304-0.16020.1558-0.04610.00860.1165-0.03160.10465.191290.149824.6421
88.9093.78792.21233.7491.25032.37870.17650.0667-0.18640.09450.1383-0.63010.2240.3344-0.31470.27680.0301-0.11270.196-0.08310.282515.349768.084529.393
94.89421.95670.4913.90490.45340.0759-0.12060.16510.08240.09630.1089-0.01950.01010.0060.01170.0422-0.01930.00850.049-0.01740.01412.512424.030418.019
102.90221.77780.13892.86491.43221.02850.2586-0.0338-0.0194-0.2792-0.2189-0.0562-0.3205-0.1497-0.03970.1663-0.00220.02070.0885-0.01140.00524.003283.704916.1707
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 57
2X-RAY DIFFRACTION2A58 - 123
3X-RAY DIFFRACTION3A124 - 246
4X-RAY DIFFRACTION4A247 - 286
5X-RAY DIFFRACTION5B6 - 43
6X-RAY DIFFRACTION6B44 - 113
7X-RAY DIFFRACTION7B114 - 259
8X-RAY DIFFRACTION8B260 - 286
9X-RAY DIFFRACTION9A289
10X-RAY DIFFRACTION10B289

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