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- PDB-2hk7: Crystal structure of shikimate dehydrogenase from aquifex aeolicu... -

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Basic information

Entry
Database: PDB / ID: 2hk7
TitleCrystal structure of shikimate dehydrogenase from aquifex aeolicus in complex with mercury at 2.5 angstrom resolution
ComponentsShikimate dehydrogenase
KeywordsOXIDOREDUCTASE / shikimate pathway / shikimate dehydrogenase / drug design
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 / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-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 ...Shikimate dehydrogenase / Quinate/shikimate 5-dehydrogenase/glutamyl-tRNA reductase / Shikimate / quinate 5-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
: / Shikimate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsGan, J.H. / Prabakaran, P. / Gu, Y.J. / Andrykovitch, M. / Li, Y. / Liu, H.H. / Yan, H. / Ji, X.
CitationJournal: Biochemistry / Year: 2007
Title: Structural and biochemical analyses of shikimate dehydrogenase AroE from Aquifex aeolicus: implications for the catalytic mechanism.
Authors: Gan, J. / Wu, Y. / Prabakaran, P. / Gu, Y. / Li, Y. / Andrykovitch, M. / Liu, H. / Gong, Y. / Yan, H. / Ji, X.
History
DepositionJul 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: audit_author / chem_comp_atom ...audit_author / chem_comp_atom / chem_comp_bond / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE Based on the electron density, especially the annealed omit maps, the authors believe ...SEQUENCE Based on the electron density, especially the annealed omit maps, the authors believe residue 195 in their structure is Glu and not Lys, residue 233 in their structure is Leu and not Phe, as it is in the UNP database.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Shikimate dehydrogenase
B: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4308
Polymers60,2262
Non-polymers1,2046
Water1,72996
1
A: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7154
Polymers30,1131
Non-polymers6023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7154
Polymers30,1131
Non-polymers6023
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.181, 74.928, 190.046
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Shikimate dehydrogenase


Mass: 30113.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: aroE / Plasmid: PET-17B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: O67049, shikimate dehydrogenase (NADP+)
#2: Chemical
ChemComp-HG / MERCURY (II) ION


Mass: 200.590 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Hg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 292 K / Method: soaking / pH: 6.4
Details: 0.1 mM ethyl mercuric phosphate in 0.1 M MES (pH 6.4-6.6), 12% PEG20K, Soaking, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X9B / Wavelength: 0.9918,1.0072,1.0084,1.0087
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 6, 1999
RadiationMonochromator: silicon / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.99181
21.00721
31.00841
41.00871
ReflectionResolution: 2.5→30 Å / Num. all: 17682 / Num. obs: 17682 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 41.5 Å2 / Rmerge(I) obs: 0.084 / Rsym value: 0.281 / Net I/σ(I): 14.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.507 / Mean I/σ(I) obs: 2 / % possible all: 82.9

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Processing

Software
NameVersionClassification
CNS1refinement
MADSYSphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→29.42 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 45816.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.272 829 4.9 %RANDOM
Rwork0.229 ---
obs0.229 17001 90.8 %-
all-17001 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.7105 Å2 / ksol: 0.316528 e/Å3
Displacement parametersBiso mean: 47.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2--15.08 Å20 Å2
3----14.79 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-30 Å
Luzzati sigma a0.54 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.5→29.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4250 0 6 96 4352
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.081.5
X-RAY DIFFRACTIONc_mcangle_it4.912
X-RAY DIFFRACTIONc_scbond_it4.812
X-RAY DIFFRACTIONc_scangle_it6.892.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.416 117 5.2 %
Rwork0.335 2139 -
obs--74.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4dna-rna_rep.paramdna-rna.top

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