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- PDB-3fs2: Crystal structure of 2-Dehydro-3-Deoxyphosphooctonate aldolase fr... -

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Basic information

Entry
Database: PDB / ID: 3fs2
TitleCrystal structure of 2-Dehydro-3-Deoxyphosphooctonate aldolase from Bruciella melitensis at 1.85A resolution
Components2-dehydro-3-deoxyphosphooctonate aldolase
KeywordsTRANSFERASE / SSGCID / BRUCIELLLA MELITENSIS / DAHP SYNTHETASE I / 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE / Cytoplasm / Lipopolysaccharide biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / cytoplasm
Similarity search - Function
3-deoxy-8-phosphooctulonate synthase / DAHP synthetase I/KDSA / DAHP synthetase I family / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / 2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.85 Å
AuthorsSSGCID / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of 2-Dehydro-3-Deoxyphosphooctonate aldolase from Bruciella melitensis at 1.85A resolution
Authors: SSGCID
History
DepositionJan 9, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.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: 2-dehydro-3-deoxyphosphooctonate aldolase
B: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4807
Polymers63,7072
Non-polymers7735
Water5,639313
1
A: 2-dehydro-3-deoxyphosphooctonate aldolase
B: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules

A: 2-dehydro-3-deoxyphosphooctonate aldolase
B: 2-dehydro-3-deoxyphosphooctonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,95914
Polymers127,4144
Non-polymers1,54510
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area8990 Å2
ΔGint-63 kcal/mol
Surface area34530 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-7 kcal/mol
Surface area19960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.530, 75.640, 74.650
Angle α, β, γ (deg.)90.00, 126.00, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-433-

HOH

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Components

#1: Protein 2-dehydro-3-deoxyphosphooctonate aldolase / Phospho-2-dehydro-3-deoxyoctonate aldolase / 3-deoxy-D-manno-octulosonic acid 8-phosphate ...Phospho-2-dehydro-3-deoxyoctonate aldolase / 3-deoxy-D-manno-octulosonic acid 8-phosphate synthetase / KDO-8-phosphate synthetase / KDO 8-P synthase / KDOPS


Mass: 31853.529 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: BIOVAR ABORTUS 2308 / Gene: 3787797, BMEI0850, kdsA / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8YHF1, 3-deoxy-8-phosphooctulonate synthase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.18 Å3/Da / Density % sol: 43.54 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: JCSG+ SCREEN D3: 100MM NA/K PHOSPHATE PH 6.2, 50% PEG 200, 200MM NACL, PH 5.5, VAPOR DIFFUSION, TEMPERATURE 290K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 / Wavelength: 1 Å
DetectorType: WESTBROOK NOIR / Detector: CCD / Date: Oct 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 1.85→50 Å / Num. all: 45916 / Num. obs: 45916 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.22
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 2.6 / Num. unique all: 3021 / % possible all: 87.1

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.5.0070refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: molecular replacement
Starting model: pdb coordinate set 1fws, monomer after sidechain adjustment with chainsaw

1fws


Resolution: 1.85→19.17 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.826 / SU ML: 0.085 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2366 5.2 %RANDOM
Rwork0.176 ---
all0.179 45914 --
obs0.179 45914 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.39 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å20 Å20.18 Å2
2--0.39 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3778 0 40 313 4131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223880
X-RAY DIFFRACTIONr_bond_other_d0.0010.022579
X-RAY DIFFRACTIONr_angle_refined_deg1.5911.9815257
X-RAY DIFFRACTIONr_angle_other_deg0.99336341
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9945506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92424.476143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10915634
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2411519
X-RAY DIFFRACTIONr_chiral_restr0.0970.2625
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214267
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02726
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_it1.0071.52531
X-RAY DIFFRACTIONr_mcbond_other0.2751.51021
X-RAY DIFFRACTIONr_mcangle_it1.77324056
X-RAY DIFFRACTIONr_scbond_it2.68231349
X-RAY DIFFRACTIONr_scangle_it4.3764.51198
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 169 -
Rwork0.325 2820 -
obs--87.22 %

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