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- PDB-3o8q: 1.45 Angstrom Resolution Crystal Structure of Shikimate 5-Dehydro... -

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Basic information

Entry
Database: PDB / ID: 3o8q
Title1.45 Angstrom Resolution Crystal Structure of Shikimate 5-Dehydrogenase (aroE) from Vibrio cholerae
Components(Shikimate 5-dehydrogenase I ...) x 2
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha/beta domain
Function / homologyLeucine Dehydrogenase, chain A, domain 1 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesVibrio cholerae biovar El Tor (bacteria)
Vibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsMinasov, G. / Light, S.H. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.45 Angstrom Resolution Crystal Structure of Shikimate 5-Dehydrogenase (aroE) from Vibrio cholerae.
Authors: Minasov, G. / Light, S.H. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 18, 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 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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_alt_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Shikimate 5-dehydrogenase I alpha
B: Shikimate 5-dehydrogenase I alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1959
Polymers60,5272
Non-polymers6697
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-80 kcal/mol
Surface area23920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.871, 63.146, 136.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Shikimate 5-dehydrogenase I ... , 2 types, 2 molecules AB

#1: Protein Shikimate 5-dehydrogenase I alpha


Mass: 30552.748 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae biovar El Tor (bacteria)
Strain: N16961 / Gene: aroE, VCD_001524 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3(Magic)
References: UniProt: C3NTR0, shikimate dehydrogenase (NADP+)
#2: Protein Shikimate 5-dehydrogenase I alpha


Mass: 29974.109 Da / Num. of mol.: 1 / Mutation: Q4(PCA)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: aroE, VCD_001524 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3(Magic)
References: UniProt: C3NTR0, shikimate dehydrogenase (NADP+)

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Non-polymers , 4 types, 528 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 6.8 mGr/mL, 0.5 Sodium cloride, 0.01M Tris-HCl pH 8.3, 10 mM Curcumin; Screen: PEGs II (D1), 0.1M Sodium acetate, 0.1M HEPES pH 7.5, 22% (w/v) PEG 4000, 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: Jul 23, 2010 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.45→30 Å / Num. all: 88234 / Num. obs: 88234 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 16.4 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 25.7
Reflection shellResolution: 1.45→1.48 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.549 / Mean I/σ(I) obs: 3.2 / Num. unique all: 4378 / % 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: 1NYT

1nyt


Resolution: 1.45→29.32 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.954 / SU B: 2.25 / SU ML: 0.041 / Isotropic thermal model: Mixed, isotropic and anisotropic. / Cross valid method: THROUGHOUT / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19455 4417 5 %RANDOM
Rwork0.15182 ---
all0.15398 83518 --
obs0.15398 83518 99.83 %-
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: 15.218 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.32 Å2-0 Å2
3---0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.45→29.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4138 0 37 521 4696
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224602
X-RAY DIFFRACTIONr_bond_other_d0.0010.023126
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9666276
X-RAY DIFFRACTIONr_angle_other_deg0.95537635
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1225610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42924.218211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1115792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6211534
X-RAY DIFFRACTIONr_chiral_restr0.0910.2682
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025359
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02955
X-RAY DIFFRACTIONr_mcbond_it1.6641.52887
X-RAY DIFFRACTIONr_mcbond_other2.1981.51187
X-RAY DIFFRACTIONr_mcangle_it2.50724661
X-RAY DIFFRACTIONr_scbond_it3.68431715
X-RAY DIFFRACTIONr_scangle_it5.4144.51615
X-RAY DIFFRACTIONr_rigid_bond_restr1.87534602
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.243 301 -
Rwork0.166 6110 -
obs--99.95 %

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