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- PDB-4p4l: Crystal Structure of Mycobacterium tuberculosis Shikimate Dehydro... -

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Basic information

Entry
Database: PDB / ID: 4p4l
TitleCrystal Structure of Mycobacterium tuberculosis Shikimate Dehydrogenase
ComponentsShikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase)
KeywordsOXIDOREDUCTASE / 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
Chem-SKM / 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: 2.009 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_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 1.3Dec 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
Revision 1.4Mar 27, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)85,87011
Polymers84,8673
Non-polymers1,0038
Water1,838102
1
A: Shikimate 5-dehydrogenase AroE (5-dehydroshikimate reductase)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6554
Polymers28,2891
Non-polymers3663
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)28,5593
Polymers28,2891
Non-polymers2702
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)28,6554
Polymers28,2891
Non-polymers3663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.703, 132.315, 38.465
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-SKM / (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID / SHIKIMATE / Shikimic acid


Mass: 174.151 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H10O5
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 102 / 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: 40.27 %
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: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 26, 2012
RadiationMonochromator: Rosenbaum-Rock high-resolution double-crystal monochromator. LN2 cooled first crystal, sagittal focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 44610 / % possible obs: 99.4 % / Redundancy: 9 % / Biso Wilson estimate: 36.64 Å2 / Rmerge(I) obs: 0.066 / Χ2: 1.065 / Net I/av σ(I): 35.944 / Net I/σ(I): 8.2 / Num. measured all: 402870
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.038.90.83921760.78898.8
2.03-2.0790.73321860.8199.6
2.07-2.118.90.62822180.80599.5
2.11-2.1590.50821770.79799.5
2.15-2.290.41221740.82399.5
2.2-2.258.90.3622670.833100
2.25-2.319.10.30821600.84299.4
2.31-2.379.20.26422160.86399.5
2.37-2.449.10.22121910.8799.9
2.44-2.529.20.18122360.91799.9
2.52-2.619.20.15622120.95199.7
2.61-2.719.20.12722410.96599.9
2.71-2.849.30.11522131.06799.9
2.84-2.999.30.09422461.253100
2.99-3.179.30.07622591.40199.9
3.17-3.429.30.06422371.58199.9
3.42-3.7690.04922701.55799.7
3.76-4.318.60.03822541.50498.5
4.31-5.438.70.03122861.3397.9
5.43-508.60.02723911.26196.9

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Processing

Software
NameVersionClassification
PDB_EXTRACT3.14data extraction
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1000200656

Resolution: 2.009→46.312 Å / FOM work R set: 0.7987 / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 1918 4.48 %Random selection
Rwork0.2026 40891 --
obs0.2047 42809 94.59 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.89 Å2 / Biso mean: 47.91 Å2 / Biso min: 21.78 Å2
Refinement stepCycle: final / Resolution: 2.009→46.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5596 0 61 102 5759
Biso mean--44.39 39.77 -
Num. residues----784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085766
X-RAY DIFFRACTIONf_angle_d1.1447888
X-RAY DIFFRACTIONf_chiral_restr0.07939
X-RAY DIFFRACTIONf_plane_restr0.0061023
X-RAY DIFFRACTIONf_dihedral_angle_d12.9541955
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 (%)
2.009-2.0590.29161120.2432255236775
2.059-2.11470.28531300.24442717284790
2.1147-2.17690.32871320.2382752288491
2.1769-2.24720.27251330.22592851298493
2.2472-2.32750.26481350.2212862299795
2.3275-2.42070.29551310.21982928305995
2.4207-2.53080.29711440.21262946309097
2.5308-2.66430.30161390.21782990312997
2.6643-2.83120.25751410.22453019316098
2.8312-3.04970.28591360.21963064320099
3.0497-3.35650.25661470.21323065321299
3.3565-3.8420.23161440.1933128327299
3.842-4.83970.21541490.16753088323798
4.8397-46.32410.21781450.1963226337197
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)
15.2994-0.81650.46436.10772.74996.95260.0028-0.14-0.1149-0.15990.2966-0.5842-0.5751.1525-0.23680.2168-0.0647-0.04990.4024-0.04260.303531.8868152.9148-0.9509
27.41040.220.12644.0060.62023.4024-0.00540.20740.2011-0.3356-0.07440.0478-0.5235-0.00460.09410.35750.0143-0.04690.1993-0.02730.177918.4941159.818-3.6506
35.20140.0395-1.16422.9813-1.02995.6124-0.09340.0337-0.0716-0.23270.19341.0092-0.1756-0.8557-0.03970.1835-0.012-0.03790.40690.0510.43576.2706145.77919.146
44.1814-0.0653.0644.644-0.43274.7132-0.1196-1.2389-0.39220.9022-0.00260.94310.489-1.35510.00230.3152-0.0274-0.02511.0020.04640.84111.1514143.017618.8244
54.6636-3.35580.37383.67920.63728.4187-0.1944-0.44290.0270.43580.23910.29570.122-0.0107-0.08840.219-0.04510.01880.2183-0.01240.309316.8349140.349718.8796
62.12091.0941-1.99432.18340.55417.8555-0.1312-0.0655-0.5528-0.0395-0.1552-0.01640.56790.50160.2210.30660.02830.01760.2987-0.03540.36225.7203142.9304-1.4372
74.0855-0.0642-1.70296.2813-1.51533.17730.1833-0.2605-0.5253-0.38060.40530.54341.609-1.4293-0.56160.7881-0.1854-0.10310.54230.15790.50814.0727107.8842-1.9827
86.11650.42211.55875.0446-1.19941.42060.42250.4771-0.315-0.2666-0.0998-0.06960.89830.4845-0.27170.78440.2103-0.01530.4359-0.01610.387828.9784106.1957-3.543
95.7492-2.28662.29124.49451.01053.65290.08620.0260.32250.20150.0548-0.61680.38191.4327-0.06720.34180.07370.06250.5931-0.01690.416235.5973120.92628.6963
103.72290.4883-0.30551.70470.46297.89140.2416-0.6697-0.6440.0690.3923-1.1281.22571.8965-0.28250.51640.24530.06590.9212-0.21451.259343.9062114.70839.9607
113.309-1.4701-0.44997.5207-1.04075.7114-0.0143-0.4351-0.21760.48240.0758-0.52570.12350.4178-0.03230.26180.0161-0.01140.28350.03240.324728.3663123.920219.0305
121.66291.3491.7764.3255-0.19962.70260.05710.02890.2887-0.4357-0.03660.0546-0.0799-0.87010.0540.37440.05690.00960.44020.08570.435718.066121.2859-1.7024
135.1807-0.3859-0.01985.53590.45223.40220.06970.1228-0.1063-0.30210.2527-0.0653-0.33950.1482-0.27250.3321-0.06660.01720.2928-0.00380.198268.0778157.1156-1.3658
142.7541-1.21770.91372.2242-1.30295.36250.0897-0.32990.11330.08210.19130.4661-0.0685-0.8391-0.25690.2729-0.05590.02290.41210.01450.455953.1327144.339416.1415
152.29881.4638-1.04123.6477-0.59628.58330.0722-0.0796-0.4929-0.2195-0.06680.05950.34530.52890.05620.31910.00740.00560.3157-0.03850.422869.0282142.95020.102
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 44 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 104 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 105 through 163 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 164 through 184 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 185 through 235 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 236 through 268 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 5 through 64 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 65 through 104 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 105 through 150 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 151 through 172 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 173 through 235 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 236 through 268 )B0
13X-RAY DIFFRACTION13chain 'C' and (resid 5 through 104 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 105 through 235 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 236 through 268 )C0

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