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- PDB-1zha: A. aeolicus KDO8PS R106G mutant in complex with PEP and R5P -

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Basic information

Entry
Database: PDB / ID: 1zha
TitleA. aeolicus KDO8PS R106G mutant in complex with PEP and R5P
Components2-dehydro-3-deoxyphosphooctonate aldolase
KeywordsTRANSFERASE / KDSA KDO8PS loops catalysis conformations
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 / FOURIER SYNTHESIS / Resolution: 1.74 Å
AuthorsXu, X. / Kona, F. / Wang, J. / Lu, J. / Stemmler, T. / Gatti, D.L.
CitationJournal: Biochemistry / Year: 2005
Title: The Catalytic and Conformational Cycle of Aquifex aeolicus KDO8P Synthase: Role of the L7 Loop.
Authors: Xu, X. / Kona, F. / Wang, J. / Lu, J. / Stemmler, T. / Gatti, D.L.
History
DepositionApr 25, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)60,2358
Polymers59,3492
Non-polymers8866
Water8,863492
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)120,46916
Polymers118,6974
Non-polymers1,77212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area15880 Å2
ΔGint-119 kcal/mol
Surface area33970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)84.726, 84.726, 160.433
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-3407-

HOH

DetailsThe asymmetric unit contains a dimer. The biological assembly is a tetramer, which can be obtained by application of the symmetry operation y,x,-z

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Components

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Protein / Sugars , 2 types, 3 molecules AB

#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: 29674.266 Da / Num. of mol.: 2 / Mutation: r106g
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: kdsA / Plasmid: pet28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Keywords: subunit A and B
References: UniProt: O66496, 3-deoxy-8-phosphooctulonate synthase
#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, 497 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.: 492 / 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: 51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 4K, Na-acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE
RadiationMonochromator: confocal mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.74→43.22 Å / Num. all: 69105 / Num. obs: 57173 / % possible obs: 82.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.6 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 5.1

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Processing

Software
NameVersionClassification
CrystalCleardata collection
d*TREKdata reduction
CNSrefinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB Entry 1T96

1t96


Resolution: 1.74→43.22 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.239 5488 -random
Rwork0.207 ---
all-69105 --
obs-57173 81.6 %-
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1-3.25 Å23.25 Å2-6.49 Å2
2--2.2 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 1.74→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4021 0 41 492 4554
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d28
X-RAY DIFFRACTIONx_improper_angle_d0

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