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- PDB-4p4n: Crystal Structure of Mycobacterium tuberculosis Shikimate Dehydro... -

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Basic information

Entry
Database: PDB / ID: 4p4n
TitleCrystal Structure of Mycobacterium tuberculosis Shikimate Dehydrogenase
ComponentsShikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase)
KeywordsOXIDOREDUCTASE / Mycobacterium tuberculosis / 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
Probable shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase) / Shikimate 5-dehydrogenase
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 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: 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: Advisory / Author supporting evidence ...Advisory / 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 / pdbx_validate_symm_contact
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 / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_atom_id_1 / _pdbx_validate_symm_contact.auth_comp_id_1 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)
C: Shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,3488
Polymers84,8673
Non-polymers4805
Water6,233346
1
A: Shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5774
Polymers28,2891
Non-polymers2883
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)28,3852
Polymers28,2891
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3852
Polymers28,2891
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.568, 132.696, 38.612
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 28289.133 Da / Num. of mol.: 3
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-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.06 Å3/Da / Density % sol: 40.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.1 M sodium citrate pH 6.2, 1.65 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: 0.979 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 18, 2012
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 49226 / % possible obs: 99.3 % / Redundancy: 4.4 % / Biso Wilson estimate: 20.44 Å2 / Rmerge(I) obs: 0.057 / Χ2: 1.782 / Net I/av σ(I): 34.836 / Net I/σ(I): 15 / Num. measured all: 217954
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.95-1.984.20.17523541.22498.7
1.98-2.024.40.16424411.24199.8
2.02-2.064.40.13824331.23499.8
2.06-2.14.40.12424321.272100
2.1-2.154.40.10824701.28499.9
2.15-2.24.50.10223971.45499.8
2.2-2.254.50.09224621.39399.8
2.25-2.314.50.08424171.41999.7
2.31-2.384.60.08124491.42100
2.38-2.464.50.07724611.5699.8
2.46-2.544.60.07424541.78399.9
2.54-2.654.50.07124491.99399.6
2.65-2.774.60.06724852.12299.8
2.77-2.914.50.0624412.03799.6
2.91-3.14.50.05324682.02899.4
3.1-3.334.50.05124592.23998.8
3.33-3.674.30.0524502.72997.8
3.67-4.24.20.04725172.88698.9
4.2-5.294.30.0425152.38998.4
5.29-504.30.03726721.93497.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4P4G

4p4g


Resolution: 1.95→46.168 Å / FOM work R set: 0.8474 / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 2494 5.07 %Random selection
Rwork0.1861 46660 --
obs0.1883 49154 99.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.8 Å2 / Biso mean: 22.96 Å2 / Biso min: 7.3 Å2
Refinement stepCycle: final / Resolution: 1.95→46.168 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5614 0 25 346 5985
Biso mean--27.55 27.49 -
Num. residues----788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075751
X-RAY DIFFRACTIONf_angle_d1.127869
X-RAY DIFFRACTIONf_chiral_restr0.071930
X-RAY DIFFRACTIONf_plane_restr0.0061025
X-RAY DIFFRACTIONf_dihedral_angle_d11.5311957
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.9840.27151290.17882484261398
1.984-2.02450.26851350.180725852720100
2.0245-2.06860.24321330.182825392672100
2.0686-2.11670.22541250.188325922717100
2.1167-2.16960.24891390.172725752714100
2.1696-2.22830.26141570.179125422699100
2.2283-2.29380.24171490.180125672716100
2.2938-2.36790.21671340.183825762710100
2.3679-2.45250.25691410.186825962737100
2.4525-2.55070.20761340.187425832717100
2.5507-2.66680.281330.194725872720100
2.6668-2.80730.23851250.199926032728100
2.8073-2.98320.24021570.203226202777100
2.9832-3.21350.23491380.20322602274099
3.2135-3.53680.23221340.19352578271298
3.5368-4.04830.21961420.17212599274199
4.0483-5.09940.18261530.16292631278498
5.0994-46.18110.20711360.19992801293798
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)
12.392-0.8811-0.03012.1970.43380.9346-0.05880.00070.1703-0.00410.0307-0.1288-0.04440.06250.04270.12110.0112-0.02140.0812-0.01070.091123.5242157.0694-2.2813
20.6072-0.01250.29110.2524-0.42382.65880.0243-0.1517-0.0356-0.0390.05930.06640.1828-0.2923-0.06960.138-0.0172-0.01280.1029-0.00630.166912.48143.43411.4241
32.0212-1.08261.2971.7724-0.61163.51770.2788-0.0868-0.4654-0.09590.10690.16730.2652-0.433-0.17670.13520.0032-0.02370.19190.04990.187224.251110.78390.1667
40.6890.3704-0.20861.46791.18653.36150.0892-0.0738-0.06740.09910.0587-0.1839-0.17220.053-0.08250.13670.04690.00050.11840.0290.158728.9261121.176211.3129
51.69460.6414-0.44482.43710.37741.8102-0.02870.00620.1655-0.14830.03690.0879-0.00370.08990.02210.11730.0042-0.0050.1120.01930.090167.4747157.5349-1.177
60.3721-0.1186-0.12220.7876-0.5972.3475-0.0271-0.0463-0.0585-0.0032-0.01950.10990.0342-0.14910.04160.1087-0.02930.00110.1083-0.02540.147355.8949144.292712.9643
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 268 )A0
3X-RAY DIFFRACTION3chain 'B' and (resid 5 through 150 )B0
4X-RAY DIFFRACTION4chain 'B' and (resid 151 through 265 )B0
5X-RAY DIFFRACTION5chain 'C' and (resid 5 through 104 )C0
6X-RAY DIFFRACTION6chain 'C' and (resid 105 through 267 )C0

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