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- PDB-4xij: Crystal Structure of a Shikimate 5-dehydrogenase from Mycobacteri... -

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Basic information

Entry
Database: PDB / ID: 4xij
TitleCrystal Structure of a Shikimate 5-dehydrogenase from Mycobacterium fortuitum Determined by Iodide SAD Phasing
ComponentsShikimate 5-dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Mycobacterium fortuitum / Shikimate 5-dehydrogenase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / cytoplasm
Similarity search - Function
Shikimate dehydrogenase, AroM-type / 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
Shikimate 5-dehydrogenase
Similarity search - Component
Biological speciesMycobacterium fortuitum subsp. fortuitum DSM 46621 (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of a Shikimate 5-dehydrogenase from Mycobacterium fortuitum Determined by Iodide SAD Phasing
Authors: SSGCID / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Lorimer, D. / Edwards, T.E.
History
DepositionJan 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Shikimate 5-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9628
Polymers28,3911
Non-polymers5707
Water7,584421
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-49 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.860, 93.860, 53.080
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Detailsbiological unit is a monomer

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Components

#1: Protein Shikimate 5-dehydrogenase


Mass: 28391.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium fortuitum subsp. fortuitum DSM 46621 (bacteria)
Gene: aroE, MFORT_30634 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: K0V1M6, shikimate dehydrogenase (NADP+)
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 421 / 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: 2.38 Å3/Da / Density % sol: 48.26 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: at 47.4mg/ml, mixed 1:1 with MCSG1(e1): 0.1M HEPES: NaOH, pH=7.5, 2M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Jan 2, 2015
RadiationMonochromator: Rigaku Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 184794 / Rmerge(I) obs: 0.041 / Χ2: 2.5 / D res high: 2 Å / Num. obs: 35184 / % possible obs: 99.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
6.328.9472110.033
5.166.3294910.035
4.475.16109410.033
44.47127110.032
3.654139910.033
3.383.65149710.034
3.163.38160410.034
2.983.16175310.038
2.832.98182510.042
2.72.83192310.045
2.582.7201810.047
2.482.58208910.049
2.392.48220010.05
2.312.39223210.056
2.242.31231610.064
2.172.24244510.066
2.112.17242610.068
2.052.11258810.073
22.05244410.074
ReflectionResolution: 1.45→50 Å / Num. obs: 46557 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 9.4 % / Biso Wilson estimate: 11.61 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.038 / Rrim(I) all: 0.04 / Χ2: 0.956 / Net I/σ(I): 34.12 / Num. measured all: 436211
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.45-1.492.60.7370.4572.167632348429740.54885.4
1.49-1.530.8430.4123.4113949341532800.46896
1.53-1.570.8860.3414.515051328232040.38597.6
1.57-1.620.9220.286.1617631321331930.3199.4
1.62-1.670.9660.2348.9322350311731150.25399.9
1.67-1.730.9860.18111.425442301130110.193100
1.73-1.80.9920.14614.1925928291929190.155100
1.8-1.870.9950.1216.5325923277627760.127100
1.87-1.960.9970.09522.4426278271326950.199.3
1.96-2.050.9980.06930.3326145255025490.072100
2.05-2.160.9990.05637.3526010243624360.059100
2.16-2.290.9990.05443.9324976233023070.05699
2.29-2.450.9990.04252.2224779217021680.04499.9
2.45-2.6510.03660.8724189203120310.037100
2.65-2.910.03168.9823714187418740.033100
2.9-3.2410.02685.7323380169216920.027100
3.24-3.7410.024105.6923559150115010.025100
3.74-4.5910.021135.2425695126712660.02299.9
4.59-6.4810.022135.8222084100210020.022100

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
ARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.45→40.643 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1768 2310 4.96 %
Rwork0.1372 44244 -
obs0.1393 46554 98.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.16 Å2 / Biso mean: 16.112 Å2 / Biso min: 6.29 Å2
Refinement stepCycle: final / Resolution: 1.45→40.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1925 0 32 423 2380
Biso mean--36.4 29.59 -
Num. residues----268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0152097
X-RAY DIFFRACTIONf_angle_d1.5892883
X-RAY DIFFRACTIONf_chiral_restr0.078332
X-RAY DIFFRACTIONf_plane_restr0.009383
X-RAY DIFFRACTIONf_dihedral_angle_d13.069770
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4499-1.47950.26491120.2092216232883
1.4795-1.51170.29061490.20272475262495
1.5117-1.54690.19741110.16212592270397
1.5469-1.58560.20521370.14862565270298
1.5856-1.62840.19341350.135326182753100
1.6284-1.67640.21081140.122326672781100
1.6764-1.73050.17061350.114726262761100
1.7305-1.79230.151370.116926332770100
1.7923-1.86410.18961150.129626722787100
1.8641-1.94890.20451410.13922602274399
1.9489-2.05170.17691640.119926282792100
2.0517-2.18020.1751540.123226272781100
2.1802-2.34850.16441470.13572626277399
2.3485-2.58480.18371340.132226312765100
2.5848-2.95880.18611090.145427032812100
2.9588-3.72730.14561580.13326602818100
3.7273-40.65850.16551580.143327032861100

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