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- PDB-3u80: 1.60 Angstrom Resolution Crystal Structure of a 3-Dehydroquinate ... -

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Basic information

Entry
Database: PDB / ID: 3u80
Title1.60 Angstrom Resolution Crystal Structure of a 3-Dehydroquinate Dehydratase-like Protein from Bifidobacterium longum
Components3-dehydroquinate dehydratase, type II
KeywordsUNKNOWN FUNCTION / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


quinate catabolic process / 3-dehydroquinate dehydratase / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
Dehydroquinase, class II / Dehydroquinase, class II, conserved site / Dehydroquinase class II signature. / Dehydroquinase, class II / Dehydroquinase, class II superfamily / Dehydroquinase class II / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-dehydroquinate dehydratase
Similarity search - Component
Biological speciesBifidobacterium longum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLight, S.H. / Minasov, G. / Shuvalova, L. / Papazisi, L. / Lavie, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Struct.Funct.Genom. / Year: 2013
Title: Crystal structure of a type II dehydroquinate dehydratase-like protein from Bifidobacterium longum.
Authors: Light, S.H. / Krishna, S.N. / Bergan, R.C. / Lavie, A. / Anderson, W.F.
History
DepositionOct 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 3-dehydroquinate dehydratase, type II
B: 3-dehydroquinate dehydratase, type II


Theoretical massNumber of molelcules
Total (without water)33,4942
Polymers33,4942
Non-polymers00
Water3,855214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-8 kcal/mol
Surface area12390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.004, 72.684, 81.713
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 3-dehydroquinate dehydratase, type II


Mass: 16747.039 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Strain: JDM301 / Gene: BLJ_0876 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D6ZTY6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / 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: 1.95 Å3/Da / Density % sol: 36.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: Protein: 8.4 mg/ml, 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3. Screen Pact B2 (Qiagen), 0.1 M MIB buffer, 25% (w/v) PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 6, 2011 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 35461 / Num. obs: 35461 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 40.8
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.503 / Mean I/σ(I) obs: 6.3 / Num. unique all: 1738 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2DHQ

2dhq


Resolution: 1.6→29.94 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.912 / SU ML: 0.051 / Cross valid method: THROUGHOUT / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2027 1772 5 %RANDOM
Rwork0.17642 ---
obs0.17783 33629 99.79 %-
all-33629 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.278 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---1.15 Å20 Å2
3---1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1930 0 0 214 2144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022128
X-RAY DIFFRACTIONr_bond_other_d0.0020.021373
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9622926
X-RAY DIFFRACTIONr_angle_other_deg0.79133414
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4355291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.1825.36197
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.69815377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.909159
X-RAY DIFFRACTIONr_chiral_restr0.0770.2342
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212399
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02394
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.6→1.639 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 109 -
Rwork0.227 2235 -
obs--98.2 %
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)
10.30070.1017-0.06720.396-0.3480.3093-0.06630.0011-0.01890.12930.0616-0.0079-0.1204-0.04950.00460.08550.01920.01340.044-0.02190.0208-0.700154.071918.3557
22.3799-0.1658-0.84180.7786-0.18360.6345-0.1791-0.02440.06580.35560.0807-0.0442-0.0010.04640.09830.17510.042-0.00290.04810.0090.05345.014151.701322.5485
30.5032-0.2235-0.12390.3719-0.17790.2401-0.036-0.0070.01770.02010.0238-0.00350.0083-0.01670.01220.01950.00320.00090.0372-0.00590.0388-3.75555.91957.4727
40.63210.1862-0.34970.71090.11220.4447-0.0641-0.0068-0.0130.08720.0225-0.02090.01320.04450.04160.05230.0031-0.00130.02980.00620.03247.636147.340210.7447
50.13050.25430.03621.5118-0.83220.814-0.0308-0.0008-0.0946-0.1363-0.017-0.26520.06410.0150.04780.03460.01710.02850.0246-0.00550.079117.669931.2181-0.2258
60.14090.2514-0.22561.2612-0.06890.5271-0.03170-0.0367-0.0272-0.0104-0.05980.07690.01740.04210.03010.01340.00370.0177-0.01050.03213.597827.51862.4322
75.77752.06528.22681.00192.416812.7744-0.21260.17680.1596-0.08620.03970.1008-0.26860.28180.17290.0314-0.02550.0010.0261-0.01660.0826-0.454722.95370.9956
80.35710.0080.12041.4329-0.28370.09830.00450.01060.0060.09710.00630.0565-0.01460.0014-0.01080.0408-0.00070.01220.0273-0.00090.02667.428936.66316.4074
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 25
2X-RAY DIFFRACTION2A26 - 49
3X-RAY DIFFRACTION3A50 - 120
4X-RAY DIFFRACTION4A121 - 148
5X-RAY DIFFRACTION5B1 - 32
6X-RAY DIFFRACTION6B33 - 80
7X-RAY DIFFRACTION7B81 - 92
8X-RAY DIFFRACTION8B93 - 148

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