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- PDB-5hvn: 3.0 Angstrom Crystal Structure of 3-dehydroquinate Synthase (AroB... -

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Basic information

Entry
Database: PDB / ID: 5hvn
Title3.0 Angstrom Crystal Structure of 3-dehydroquinate Synthase (AroB) from Francisella tularensis in Complex with NAD.
Components3-dehydroquinate synthase
KeywordsLYASE / 3-dehydroquinate synthase / NAD / Shikimate Pathway / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


3-dehydroquinate synthase / 3-dehydroquinate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / nucleotide binding / metal ion binding / cytoplasm
Similarity search - Function
3-dehydroquinate synthase family / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich ...3-dehydroquinate synthase family / 3-dehydroquinate synthase AroB / 3-dehydroquinate synthase domain / 3-dehydroquinate synthase / Dehydroquinate synthase-like, alpha domain / Dehydroquinate synthase-like - alpha domain / Rossmann fold - #1970 / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 3-dehydroquinate synthase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsMinasov, G. / Light, S.H. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Zhou, M. / Grimshaw, S. / Kwon, K. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 3.0 Angstrom Crystal Structure of 3-dehydroquinate Synthase (AroB) from Francisella tularensis in Complex with NAD.
Authors: Minasov, G. / Light, S.H. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Zhou, M. / Grimshaw, S. / Kwon, K. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-dehydroquinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1703
Polymers40,4711
Non-polymers6992
Water1,00956
1
A: 3-dehydroquinate synthase
hetero molecules

A: 3-dehydroquinate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,3406
Polymers80,9432
Non-polymers1,3984
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_554x,x-y,-z-1/21
Buried area4970 Å2
ΔGint-46 kcal/mol
Surface area30450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.978, 178.978, 96.219
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-531-

HOH

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Components

#1: Protein 3-dehydroquinate synthase /


Mass: 40471.348 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (strain SCHU S4 / Schu 4) (bacteria)
Strain: SCHU S4 / Schu 4 / Gene: aroB, FTT_1154c / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)magic / References: UniProt: Q5NFS1, 3-dehydroquinate synthase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 5.5 Å3/Da / Density % sol: 77.5 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.3
Details: Protein: 7.5 mg/ml, 0.5 M NaCl, 0.1M Tris-HCl (pH 8.3); Condition:0.2M Sodium Formate, 0.1 M Sodium Acetate (pH 5.3).

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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: Dec 10, 2009 / Details: C(111)
RadiationMonochromator: Beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 18744 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.6 % / Biso Wilson estimate: 94.6 Å2 / CC1/2: 0.887 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 40.4
Reflection shellResolution: 3→3.05 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.814 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
MoRDaphasing
BLU-MAXdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EKS

5eks


Resolution: 3→29.83 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.952 / SU B: 16.475 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.331 / ESU R Free: 0.238 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.19223 968 5.2 %RANDOM
Rwork0.15743 ---
obs0.15911 17684 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 88.967 Å2
Baniso -1Baniso -2Baniso -3
1--1.99 Å2-0.99 Å20 Å2
2---1.99 Å20 Å2
3---6.44 Å2
Refinement stepCycle: 1 / Resolution: 3→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2780 0 45 56 2881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192885
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6491.9763906
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.1965353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.77225.276127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.80515513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5159
X-RAY DIFFRACTIONr_chiral_restr0.1310.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022114
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9875.6391418
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.4378.4351769
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.6025.9921466
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined11.72947.5224423
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 91 -
Rwork0.282 1249 -
obs--100 %
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)
11.5748-1.0813-0.23784.47240.36783.69-0.1246-0.71570.34540.69420.2079-0.4616-0.30770.4125-0.08330.51420.1548-0.12550.4761-0.20470.1628-51.7703-47.2833-6.7592
23.0807-1.41430.32246.2577-2.45672.4667-0.1017-0.5374-0.06840.73350.34060.5655-0.1666-0.1056-0.23880.25430.13450.04950.2197-0.03690.0952-66.2222-45.2747-11.7773
33.0986-1.5526-0.41463.5713-0.68821.4837-0.0203-0.22870.04580.25460.0901-0.1661-0.27010.0891-0.06980.30330.0904-0.00510.1905-0.13220.1303-56.7712-45.7677-18.6566
42.7004-1.2506-1.8672.18111.1151.53780.0238-0.26990.22520.26170.2085-0.61460.02360.4474-0.23230.16680.0946-0.09590.4521-0.1610.3632-41.1926-56.5112-21.9399
51.3610.6321-1.74962.0685-0.21594.0390.03950.19530.5017-0.00370.1801-0.08020.0089-0.458-0.21960.08760.14850.03650.3564-0.01590.4135-49.7391-62.9969-36.9067
66.4782.41381.36844.12991.70557.2801-0.00950.16350.4809-0.49810.0955-0.0834-0.5855-0.5629-0.0860.17480.14650.09150.24310.05920.2524-47.3681-55.9191-45.3004
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 57
2X-RAY DIFFRACTION2A58 - 110
3X-RAY DIFFRACTION3A111 - 169
4X-RAY DIFFRACTION4A170 - 245
5X-RAY DIFFRACTION5A246 - 321
6X-RAY DIFFRACTION6A322 - 359

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