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- PDB-3pgj: 2.49 Angstrom resolution crystal structure of shikimate 5-dehydro... -

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Entry
Database: PDB / ID: 3pgj
Title2.49 Angstrom resolution crystal structure of shikimate 5-dehydrogenase (aroE) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with shikimate
ComponentsShikimate dehydrogenase
KeywordsOXIDOREDUCTASE / Shikimate 5-Dehydrogenase / Shikimate / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha/beta domain
Function / homology
Function and homology information


shikimate dehydrogenase (NADP+) / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / 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
Chem-SKM / Shikimate dehydrogenase (NADP(+))
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar eltor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsHalavaty, A.S. / Light, S.H. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 2.49 Angstrom resolution crystal structure of shikimate 5-dehydrogenase (aroE) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with shikimate
Authors: Halavaty, A.S. / Light, S.H. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionNov 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)132,7948
Polymers132,0984
Non-polymers6974
Water2,072115
1
A: Shikimate dehydrogenase
D: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3974
Polymers66,0492
Non-polymers3482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2600 Å2
ΔGint-1 kcal/mol
Surface area23410 Å2
MethodPISA
2
B: Shikimate dehydrogenase
C: Shikimate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3974
Polymers66,0492
Non-polymers3482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint-1 kcal/mol
Surface area23390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.527, 83.657, 79.585
Angle α, β, γ (deg.)90.00, 93.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Shikimate dehydrogenase /


Mass: 33024.414 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar eltor (bacteria)
Strain: N16961 / Gene: aroE, VC_0056 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/Magic
References: UniProt: Q9KVT3, 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.: 4 / Source method: obtained synthetically / Formula: C7H10O5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 1.9 Å3/Da / Density % sol: 35.25 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: Protein: 7.5 mg/mL in 10 mM Tris/HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Crystallization condition: The Classic suite H3 (#87) condition (0.2 M Ammonium acetate, 0.1 M tri-Sodium citrate pH 5.6, ...Details: Protein: 7.5 mg/mL in 10 mM Tris/HCl pH 8.3, 0.5 M NaCl, 5 mM BME. Crystallization condition: The Classic suite H3 (#87) condition (0.2 M Ammonium acetate, 0.1 M tri-Sodium citrate pH 5.6, 30 % (w/v) PEG4000). Crystal was soaked in 25 mM shikimate. , VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 20, 2010 / Details: Be-Lenses/Diamond Laue Mono
RadiationMonochromator: Diamond[111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 34293 / Num. obs: 34293 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.77
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.525 / Mean I/σ(I) obs: 2.41 / Num. unique all: 1679 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3O8Q

3o8q


Resolution: 2.49→28.8 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.935 / SU B: 22.894 / SU ML: 0.232 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24711 1723 5 %RANDOM
Rwork0.19338 ---
obs0.19609 32555 98.68 %-
all-32555 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.66 Å2
Baniso -1Baniso -2Baniso -3
1--1.5 Å20 Å20.58 Å2
2--0.42 Å20 Å2
3---1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.49→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8261 0 48 115 8424
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0228475
X-RAY DIFFRACTIONr_bond_other_d0.0010.025727
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.96211459
X-RAY DIFFRACTIONr_angle_other_deg0.825313948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg0.93851073
X-RAY DIFFRACTIONr_dihedral_angle_2_deg18.35924.308390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg5.85151429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.1981557
X-RAY DIFFRACTIONr_chiral_restr0.0830.21282
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029570
X-RAY DIFFRACTIONr_gen_planes_other00.021735
X-RAY DIFFRACTIONr_mcbond_it0.5781.55316
X-RAY DIFFRACTIONr_mcbond_other0.1071.52215
X-RAY DIFFRACTIONr_mcangle_it1.13228468
X-RAY DIFFRACTIONr_scbond_it1.84833159
X-RAY DIFFRACTIONr_scangle_it3.1034.52991
LS refinement shellResolution: 2.491→2.556 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 118 -
Rwork0.256 1991 -
obs-1991 82.61 %
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)
13.8318-1.2131-1.86424.98841.17694.0446-0.1852-0.3586-0.33660.50610.27970.12120.21560.188-0.09450.06980.08910.04830.25190.11580.27234.2868-9.824337.2569
21.78840.8541-0.93353.5074-1.4951.9215-0.13160.071-0.2936-0.31660.09930.39110.2281-0.05860.03230.03960.018-0.01290.2239-0.01270.2379.3342-2.9420.2124
32.58760.963-0.91383.0117-0.75691.77380.0637-0.20570.0034-0.0016-0.0256-0.0994-0.06270.2242-0.03810.01320.0316-0.00590.23370.01280.179417.32396.356324.8302
43.1956-0.4590.63292.8471-0.78015.45150.0303-0.03580.3288-0.17720.13670.134-0.2994-0.4289-0.16710.0736-0.02240.0920.15130.01010.3373-35.072715.2593.8884
58.1807-1.66091.32863.8831.63495.3885-0.3292-1.29530.74060.2478-0.0507-0.1111-0.2563-0.76430.37990.05040.0768-0.01230.4588-0.14190.2821-19.583912.737523.5415
66.8171-0.27674.07851.0875-0.91444.37830.12110.1182-0.0337-0.19-0.0772-0.15780.42910.3726-0.04380.12280.05330.11160.13560.00710.2599-18.1754.98927.934
75.22382.30020.01887.5897-1.774.9374-0.0892-0.072-0.04060.1198-0.02230.0270.1635-0.10880.11150.0587-0.03120.03930.10990.02310.1166-28.577912.8602-16.0135
84.9417-0.28881.16821.2256-1.41594.7825-0.14140.58710.3234-0.20680.17190.1005-0.1854-0.1333-0.03050.1914-0.1094-0.0010.33680.04620.3177-30.042223.1337-36.538
94.3287-2.77051.69038.5025-5.326.78060.11560.13050.2441-0.32890.65331.22840.1527-1.5012-0.76890.1009-0.1082-0.01620.5950.10360.5376-44.398718.8229-30.4222
106.835-1.7628-0.08865.7176-0.94583.49020.40240.36510.56-0.1795-0.5123-0.9646-0.21140.46540.10980.1153-0.00860.15280.2140.07610.35124.4608-1.336153.5346
112.70880.8225-2.05643.9547-1.94373.63640.1449-0.34060.44650.83-0.0678-0.5076-0.65760.4192-0.0770.2818-0.0312-0.0830.2917-0.15360.3091-0.3229-4.96273.6907
121.28020.3609-0.57526.569-1.4952.94880.01020.01450.06160.48310.2060.0853-0.0984-0.1571-0.21620.05880.05280.04780.2373-0.05880.2142-10.7782-13.930469.1096
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 80
2X-RAY DIFFRACTION2A81 - 152
3X-RAY DIFFRACTION3A153 - 276
4X-RAY DIFFRACTION4B5 - 121
5X-RAY DIFFRACTION5B122 - 196
6X-RAY DIFFRACTION6B197 - 275
7X-RAY DIFFRACTION7C5 - 71
8X-RAY DIFFRACTION8C72 - 202
9X-RAY DIFFRACTION9C203 - 275
10X-RAY DIFFRACTION10D5 - 75
11X-RAY DIFFRACTION11D76 - 169
12X-RAY DIFFRACTION12D170 - 275

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