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- PDB-1fww: AQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH PEP, A5P AND CADMIUM -

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Basic information

Entry
Database: PDB / ID: 1fww
TitleAQUIFEX AEOLICUS KDO8P SYNTHASE IN COMPLEX WITH PEP, A5P AND CADMIUM
Components2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
KeywordsLYASE / kdo8ps / kdo8p / kdo / PEP / A5P / beta/alpha barrel
Function / homology
Function and homology information


monosaccharide biosynthetic process / 3-deoxy-8-phosphooctulonate synthase / 3-deoxy-8-phosphooctulonate synthase activity / keto-3-deoxy-D-manno-octulosonic acid biosynthetic process / cytosol
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
ARABINOSE-5-PHOSPHATE / : / PHOSPHOENOLPYRUVATE / PHOSPHATE ION / 2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.85 Å
AuthorsDuewel, H.S. / Radaev, S. / Wang, J. / Woodard, R.W. / Gatti, D.L.
CitationJournal: Biochemistry / Year: 2009
Title: Electronic structure of the metal center in the Cd(2+), Zn(2+), and Cu(2+) substituted forms of KDO8P synthase: implications for catalysis.
Authors: Kona, F. / Tao, P. / Martin, P. / Xu, X. / Gatti, D.L.
History
DepositionSep 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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.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_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

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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)60,4378
Polymers59,5492
Non-polymers8886
Water3,657203
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)120,87416
Polymers119,0984
Non-polymers1,77612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area16780 Å2
ΔGint-115 kcal/mol
Surface area33460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.108, 84.108, 159.780
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Cell settingtrigonal
Space group name H-MP3121
DetailsThe biological assembly is a tetramer constructed from chain A and chain B and their symmetry partners generated by application of the symmetry operation (x=y, y=x, z=-z)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE / E.C.4.1.2.16 / KDO8P SYNTHASE / PHOSPHO-2-DEHYDRO-3-DEOXYOCTONATE ALDOLASE / 3-DEOXY-D-MANNO-OCTULOSONIC ACID 8- ...KDO8P SYNTHASE / PHOSPHO-2-DEHYDRO-3-DEOXYOCTONATE ALDOLASE / 3-DEOXY-D-MANNO-OCTULOSONIC ACID 8-PHOSPHATE SYNTHETASE / KDO-8-PHOSPHATE SYNTHETASE


Mass: 29774.406 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Plasmid: PAAKDSA / Production host: Escherichia coli (E. coli) / References: UniProt: O66496, EC: 4.1.2.16

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Non-polymers , 5 types, 209 molecules

#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#3: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O6P
#4: Chemical ChemComp-A5P / ARABINOSE-5-PHOSPHATE


Mass: 232.126 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H13O8P
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / 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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 100 mM Na-acetate, 6% PEG 4000, pH 4.8, VAPOR DIFFUSION, HANGING DROP at 278K, temperature 278.0K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion
Details: drop contains protein and reservoir solution in a 1:1 ratio
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlenzyme1drop
2100 mMsodium acetate1reservoir
35-6 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 12, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.85→27.13 Å / Num. all: 51825 / Num. obs: 51825 / % possible obs: 91.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 17.3
Reflection shellResolution: 1.85→1.97 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.576 / Num. unique all: 5605 / % possible all: 60.1
Reflection
*PLUS
Lowest resolution: 27 Å / Num. measured all: 763003
Reflection shell
*PLUS
% possible obs: 60.1 %

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Processing

Software
NameVersionClassification
CNS1refinement
SCALEPACKdata scaling
RefinementResolution: 1.85→27.13 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 608354.09 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 5271 10.2 %RANDOM
Rwork0.205 ---
all-51825 --
obs-51825 91.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.45 Å2 / ksol: 0.349 e/Å3
Displacement parametersBiso mean: 36 Å2
Baniso -1Baniso -2Baniso -3
1-4.52 Å23.71 Å20 Å2
2--4.52 Å20 Å2
3----9.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 1.85→27.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 41 203 4322
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it1.92
X-RAY DIFFRACTIONc_scbond_it1.982
X-RAY DIFFRACTIONc_scangle_it2.912.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.459 554 9.9 %
Rwork0.412 5051 -
obs--60.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4PEP_A5P_MOD4.PARAMPEP_A5P.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87

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