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- PDB-1jcy: Aquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium -

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Basic information

Entry
Database: PDB / ID: 1jcy
TitleAquifex aeolicus KDO8P synthase in complex with R5P, PEP and Cadmium
Components2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE
KeywordsLYASE / kdo8ps / kdo8p / kdo / R5P / PEP / 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
: / PHOSPHOENOLPYRUVATE / PHOSPHATE ION / RIBOSE-5-PHOSPHATE / 2-dehydro-3-deoxyphosphooctonate aldolase
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsWang, J. / Duewel, H.S. / Woodard, R.W. / Gatti, D.L.
CitationJournal: Biochemistry / Year: 2001
Title: Structures of Aquifex aeolicus KDO8P synthase in complex with R5P and PEP, and with a bisubstrate inhibitor: role of active site water in catalysis.
Authors: Wang, J. / Duewel, H.S. / Woodard, R.W. / Gatti, D.L.
History
DepositionJun 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: 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_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_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)60,4358
Polymers59,5492
Non-polymers8866
Water3,621201
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)120,87016
Polymers119,0984
Non-polymers1,77212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area16810 Å2
ΔGint-110 kcal/mol
Surface area33560 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.316, 84.316, 159.569
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
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 / Sugars , 2 types, 3 molecules AB

#1: Protein 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE / 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
#2: Sugar ChemComp-R5P / RIBOSE-5-PHOSPHATE / Ribose 5-phosphate


Type: saccharideCarbohydrate / Mass: 230.110 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P

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Non-polymers , 4 types, 206 molecules

#3: Chemical ChemComp-CD / CADMIUM ION


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


Mass: 168.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O6P
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.75 Å3/Da / Density % sol: 55.25 %
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, temperature 278K
Crystal grow
*PLUS
Temperature: 4 ℃ / Details: Duewel, H.S., (2001) J. Biol. Chem., 276, 8393.
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 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→27 Å / Num. all: 419681 / Num. obs: 419681 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 21.4
Reflection shellResolution: 1.9→2.02 Å
Reflection
*PLUS
Lowest resolution: 27 Å / Num. obs: 46090 / Num. measured all: 419681

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Processing

Software
NameClassification
CNSrefinement
SCALEPACKdata scaling
RefinementResolution: 1.9→27 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 728459.56 / 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
Rfree0.231 4658 10.1 %RANDOM
Rwork0.202 ---
all-419681 --
obs-419681 87.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.21 Å2 / ksol: 0.3591 e/Å3
Displacement parametersBiso mean: 36.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.51 Å25.05 Å20 Å2
2--4.51 Å20 Å2
3----9.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 1.9→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4078 0 41 201 4320
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4 590 10.2 %
Rwork0.376 5205 -
obs--67.2 %
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 DIFFRACTION4r5p_pep_mimo.paramr5p_pep_mimo.toph
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 27 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.202
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.81
X-RAY DIFFRACTIONc_mcbond_it1.31.5
X-RAY DIFFRACTIONc_scbond_it2.042
X-RAY DIFFRACTIONc_mcangle_it1.992
X-RAY DIFFRACTIONc_scangle_it3.072.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.4 / % reflection Rfree: 10.2 % / Rfactor Rwork: 0.376

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