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- PDB-4p4g: Crystal Structure of Mycobacterium tuberculosis Shikimate Dehydro... -

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Basic information

Entry
Database: PDB / ID: 4p4g
TitleCrystal Structure of Mycobacterium tuberculosis Shikimate Dehydrogenase
ComponentsShikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase)
KeywordsOXIDOREDUCTASE / shikimate dehydrogenase / AroE / Structural Genomics / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


shikimate dehydrogenase (NADP+) / shikimate 3-dehydrogenase (NADP+) activity / shikimate metabolic process / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / NADP binding / protein homodimerization activity / cytosol
Similarity search - Function
Shikimate dehydrogenase, AroM-type / 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, AroM-type / 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
BROMIDE ION / Chem-SKM / Probable shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase) / Shikimate 5-dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsLalgondar, M. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Crystal Structure of Mycobacterium tuberculosis Shikimate Dehydrogenase
Authors: Lalgondar, M. / Sacchettini, J.C.
History
DepositionMar 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase)
B: Shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,60013
Polymers56,5782
Non-polymers1,02211
Water8,917495
1
A: Shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,13510
Polymers28,2891
Non-polymers8469
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4653
Polymers28,2891
Non-polymers1762
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.467, 75.553, 129.708
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase) / Shikimate 5-dehydrogenase


Mass: 28289.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: aroE, MT2629, Rv2552c / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P95001, UniProt: I6Y120*PLUS, shikimate dehydrogenase (NADP+)
#2: Chemical ChemComp-SKM / (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID / SHIKIMATE / Shikimic acid


Mass: 174.151 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H10O5
#3: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Br
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 495 / 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: 1.98 Å3/Da / Density % sol: 38.03 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.08 M sodium citrate pH 6.2, 1.54 M (NH4)2SO4, 2.7 % 1,6-hexanediol, 0.1 M guanidine HCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.92 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 22, 2012
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 47838 / % possible obs: 99.1 % / Redundancy: 7.3 % / Biso Wilson estimate: 15.24 Å2 / Rmerge(I) obs: 0.088 / Χ2: 1.554 / Net I/av σ(I): 27.4 / Net I/σ(I): 9.8 / Num. measured all: 656357
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.7-1.734.40.60840961.25589.9
1.73-1.764.80.55142621.23194.5
1.76-1.795.60.52445071.3398.2
1.79-1.836.30.50645331.37799.3
1.83-1.8770.45845291.38100
1.87-1.917.40.37745591.446100
1.91-1.967.60.32345721.388100
1.96-2.027.70.26245491.426100
2.02-2.077.70.21345931.402100
2.07-2.147.80.17945401.38100
2.14-2.227.80.15245561.42100
2.22-2.317.80.12745691.396100
2.31-2.417.80.11945591.411100
2.41-2.547.80.10845171.564100
2.54-2.77.80.09545921.824100
2.7-2.917.80.07845751.766100
2.91-3.27.90.05845221.839100
3.2-3.667.90.04745671.973100
3.66-4.617.90.03945662.001100
4.61-507.80.03745721.783100

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementMethod to determine structure: SAD / Resolution: 1.7→49.21 Å / FOM work R set: 0.8646 / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.35 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2281 1970 4.17 %Random selection
Rwork0.1846 45262 --
obs0.1864 47232 98.21 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.01 Å2 / Biso mean: 18.57 Å2 / Biso min: 3.32 Å2
Refinement stepCycle: final / Resolution: 1.7→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 34 495 4272
Biso mean--28 33.16 -
Num. residues----525
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063843
X-RAY DIFFRACTIONf_angle_d1.1035259
X-RAY DIFFRACTIONf_chiral_restr0.068626
X-RAY DIFFRACTIONf_plane_restr0.006684
X-RAY DIFFRACTIONf_dihedral_angle_d11.8381307
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.74020.27021270.23632895302289
1.7402-1.78730.25681290.21713057318695
1.7873-1.83980.25361340.19923147328197
1.8398-1.89920.21971410.17363177331898
1.8992-1.96710.20871390.1673194333399
1.9671-2.04590.19721410.16873229337099
2.0459-2.1390.22231420.172332483390100
2.139-2.25180.19451430.173832573400100
2.2518-2.39280.2341420.174732673409100
2.3928-2.57760.25361420.185632903432100
2.5776-2.83690.24821440.194532963440100
2.8369-3.24740.2131450.182933193464100
3.2474-4.09110.22551470.171533663513100
4.0911-49.23110.23181540.235203674100
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)
11.6255-0.2214-0.66071.1359-0.20582.05270.0014-0.06830.09180.05490.0322-0.0375-0.10440.01350.01760.0575-0.0099-0.00990.0383-0.01040.060224.610939.533155.9614
22.2498-0.4836-0.43761.63610.35730.71660.0213-0.001-0.0912-0.0242-0.03660.13210.0241-0.10730.00840.0745-0.0059-0.02190.09070.00780.065910.331623.047443.3248
30.8122-0.1001-0.39623.88451.20181.79110.06130.0630.1085-0.0899-0.02350.0256-0.0631-0.0283-0.01260.0704-0.0063-0.00590.07940.02270.075226.341739.447541.928
41.5034-0.53020.45520.5095-0.32121.67880.06370.16590.0716-0.0694-0.1009-0.04560.06260.10370.02140.06750.01010.00990.04310.00370.07013.769934.883272.1135
53.4088-0.85510.71762.47950.29313.2545-0.03940.07560.0255-0.0296-0.04020.0907-0.0856-0.10820.02610.07660.0026-0.00610.0925-0.00930.0783-13.236946.199884.9134
62.26531.020.36822.11510.81971.7078-0.09040.01820.236-0.1062-0.06220.2266-0.1807-0.20510.08760.11470.0161-0.00940.09450.0090.1017-10.794753.722885.7476
71.39380.1561-0.02633.58910.77972.2026-0.0039-0.020.13430.0920.01760.0658-0.0439-0.0565-0.01610.04530.00470.00030.05440.00950.0584.972636.573686.1965
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 104 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 105 through 235 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 236 through 268 )A0
4X-RAY DIFFRACTION4chain 'B' and (resid 5 through 104 )B0
5X-RAY DIFFRACTION5chain 'B' and (resid 105 through 150 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 151 through 235 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 236 through 268 )B0

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