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- PDB-5dzs: 1.5 Angstrom Crystal Structure of Shikimate Dehydrogenase 1 from ... -

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Basic information

Entry
Database: PDB / ID: 5dzs
Title1.5 Angstrom Crystal Structure of Shikimate Dehydrogenase 1 from Peptoclostridium difficile.
ComponentsShikimate dehydrogenase (NADP(+))
KeywordsOXIDOREDUCTASE / shikimate dehydrogenase 1 / CSGID / Structural genomics / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / shikimate metabolic process / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / NADP binding / cytosol
Similarity search - Function
Shikimate dehydrogenase / Shikimate dehydrogenase family / 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
Shikimate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesPeptoclostridium difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMinasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.5 Angstrom Crystal Structure of Shikimate Dehydrogenase 1 from Peptoclostridium difficile.
Authors: Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Flores, K. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 26, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Shikimate dehydrogenase (NADP(+))
B: Shikimate dehydrogenase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4785
Polymers62,1902
Non-polymers2883
Water7,620423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1380 Å2
ΔGint-6 kcal/mol
Surface area23670 Å2
2
A: Shikimate dehydrogenase (NADP(+))
hetero molecules

B: Shikimate dehydrogenase (NADP(+))
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4785
Polymers62,1902
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area1720 Å2
ΔGint-18 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.221, 47.053, 74.736
Angle α, β, γ (deg.)77.98, 76.44, 89.09
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Shikimate dehydrogenase (NADP(+))


Mass: 31094.996 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Peptoclostridium difficile (strain 630) (bacteria)
Strain: 630 / Gene: aroE1, CD630_18370 / Plasmid: pMCSG28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic
References: UniProt: Q187E7, shikimate dehydrogenase (NADP+)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 10.6 mg/ml, 0.01M Tris-HCL (pH 8.3); Screen: Classics II (F3), 0.064M Sodium citrate (pH 7.0), 0.1M HEPES (pH 7.0), 10% (w/v) PEG 5000 MME; Cryo: 1:1 (v/v), 50% Sucrose : screen solution.
PH range: 7

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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: Jun 22, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 82004 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.038 / Rsym value: 0.038 / Net I/σ(I): 29
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 4 % / Rmerge(I) obs: 0.454 / Mean I/σ(I) obs: 3.1 / % possible all: 94.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
BLU-MAXdata collection
HKL-3000data reduction
HKL-3000data scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3FBT

3fbt


Resolution: 1.5→29.7 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.641 / SU ML: 0.048 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1846 4078 5 %RANDOM
Rwork0.16345 ---
obs0.16451 77919 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.531 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20.2 Å2-0.15 Å2
2---0.91 Å2-0.46 Å2
3---0.71 Å2
Refinement stepCycle: 1 / Resolution: 1.5→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4200 0 15 423 4638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194758
X-RAY DIFFRACTIONr_bond_other_d0.0010.024704
X-RAY DIFFRACTIONr_angle_refined_deg1.3731.9816459
X-RAY DIFFRACTIONr_angle_other_deg0.754310895
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0875621
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25725.25200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.86715929
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5641518
X-RAY DIFFRACTIONr_chiral_restr0.0860.2719
X-RAY DIFFRACTIONr_gen_planes_refined0.020.025483
X-RAY DIFFRACTIONr_gen_planes_other0.0160.021043
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7282.2752376
X-RAY DIFFRACTIONr_mcbond_other1.7272.2732375
X-RAY DIFFRACTIONr_mcangle_it2.7153.3913033
X-RAY DIFFRACTIONr_mcangle_other2.7153.3943034
X-RAY DIFFRACTIONr_scbond_it2.5052.5982382
X-RAY DIFFRACTIONr_scbond_other2.4492.5912371
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.813.7713409
X-RAY DIFFRACTIONr_long_range_B_refined7.64619.9475806
X-RAY DIFFRACTIONr_long_range_B_other7.46319.0515553
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 289 -
Rwork0.229 5604 -
obs--93.24 %
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)
10.9946-0.0379-0.09831.2726-0.00030.90030.0232-0.0692-0.00740.0975-0.0269-0.0411-0.06860.00220.00380.0292-0.00190.00460.008-0.00040.008823.974631.986822.3658
24.2738-1.97741.3093.5394-0.82963.40990.2362-0.26520.35040.4569-0.3079-0.1607-0.12080.10450.07170.2203-0.0093-0.0120.263-0.08420.052519.688142.979644.5351
31.09070.27490.46091.4334-0.44941.3150.1-0.35480.19110.2063-0.00570.1604-0.1145-0.1996-0.09430.0654-0.00650.03150.1723-0.0390.07818.791136.417132.376
40.7070.14690.11542.07780.14781.23310.02910.0544-0.0036-0.1021-0.0414-0.10230.05570.01840.01230.02080.00560.02150.0115-0.00160.029526.535959.54689.9114
56.11872.1842-2.14932.7051-0.69983.70230.26810.2154-0.4283-0.361-0.2844-0.27140.04510.13150.01630.23890.0210.04910.1581-0.03870.062628.398147.643-12.8262
61.8560.1352-0.24131.93840.2811.8910.08950.37460.0389-0.3893-0.05210.1586-0.2496-0.2937-0.03740.12040.0311-0.02050.1533-0.010.040214.020254.545-2.7947
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 100
2X-RAY DIFFRACTION2A101 - 215
3X-RAY DIFFRACTION3A216 - 270
4X-RAY DIFFRACTION4B1 - 104
5X-RAY DIFFRACTION5B105 - 206
6X-RAY DIFFRACTION6B207 - 270

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