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- PDB-2qjg: M. jannaschii ADH synthase complexed with F1,6P -

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Basic information

Entry
Database: PDB / ID: 2qjg
TitleM. jannaschii ADH synthase complexed with F1,6P
ComponentsPutative aldolase MJ0400
KeywordsLYASE / beta-alpha barrel
Function / homology
Function and homology information


2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase / transketolase or transaldolase activity / fructose-bisphosphate aldolase activity / hydro-lyase activity / aromatic amino acid family biosynthetic process / amino acid biosynthetic process
Similarity search - Function
2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase / Aldolase FbaB-like, archaeal-type / : / DeoC/LacD family aldolase / DeoC/FbaB/LacD aldolase / DeoC/LacD family aldolase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1,6-DI-O-PHOSPHONO-D-ALLITOL / 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonate synthase
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsEalick, S.E. / Morar, M.
CitationJournal: Biochemistry / Year: 2007
Title: Structure of 2-amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid synthase, a catalyst in the archaeal pathway for the biosynthesis of aromatic amino acids.
Authors: Morar, M. / White, R.H. / Ealick, S.E.
History
DepositionJul 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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: Putative aldolase MJ0400
B: Putative aldolase MJ0400
C: Putative aldolase MJ0400
D: Putative aldolase MJ0400
E: Putative aldolase MJ0400
K: Putative aldolase MJ0400
L: Putative aldolase MJ0400
M: Putative aldolase MJ0400
N: Putative aldolase MJ0400
O: Putative aldolase MJ0400
F: Putative aldolase MJ0400
G: Putative aldolase MJ0400
H: Putative aldolase MJ0400
I: Putative aldolase MJ0400
J: Putative aldolase MJ0400
P: Putative aldolase MJ0400
Q: Putative aldolase MJ0400
R: Putative aldolase MJ0400
S: Putative aldolase MJ0400
T: Putative aldolase MJ0400
hetero molecules


Theoretical massNumber of molelcules
Total (without water)601,22640
Polymers594,38420
Non-polymers6,84320
Water11,133618
1
A: Putative aldolase MJ0400
B: Putative aldolase MJ0400
C: Putative aldolase MJ0400
D: Putative aldolase MJ0400
E: Putative aldolase MJ0400
K: Putative aldolase MJ0400
L: Putative aldolase MJ0400
M: Putative aldolase MJ0400
N: Putative aldolase MJ0400
O: Putative aldolase MJ0400
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,61320
Polymers297,19210
Non-polymers3,42110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area41800 Å2
ΔGint-234 kcal/mol
Surface area82500 Å2
MethodPISA, PQS
2
F: Putative aldolase MJ0400
G: Putative aldolase MJ0400
H: Putative aldolase MJ0400
I: Putative aldolase MJ0400
J: Putative aldolase MJ0400
P: Putative aldolase MJ0400
Q: Putative aldolase MJ0400
R: Putative aldolase MJ0400
S: Putative aldolase MJ0400
T: Putative aldolase MJ0400
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,61320
Polymers297,19210
Non-polymers3,42110
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42160 Å2
ΔGint-223 kcal/mol
Surface area83370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.450, 102.770, 156.410
Angle α, β, γ (deg.)89.40, 85.83, 82.05
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative aldolase MJ0400


Mass: 29719.182 Da / Num. of mol.: 20
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Production host: Escherichia coli (E. coli)
References: UniProt: Q57843, Lyases; Carbon-oxygen lyases; Hydro-lyases
#2: Chemical
ChemComp-F2P / 1,6-DI-O-PHOSPHONO-D-ALLITOL


Mass: 342.132 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C6H16O12P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 6% 1,4-butanediol, 0.1M sodium acetate, pH 4.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→46.31 Å / Num. all: 169078 / Num. obs: 159934 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 31.9 Å2
Reflection shellResolution: 2.6→2.76 Å / % possible all: 69.1

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→46.31 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 96098.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.244 8021 5 %RANDOM
Rwork0.204 ---
all0.204 169078 --
obs0.204 159934 89.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.7159 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 42 Å2
Baniso -1Baniso -2Baniso -3
1--6.52 Å26.85 Å2-1.1 Å2
2--15.76 Å23.59 Å2
3----9.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.6→46.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms40025 0 380 618 41023
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_improper_angle_d1.58
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.362 994 4.8 %
Rwork0.313 19602 -
obs-19602 69.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1temp092xxxxxxx.paramtemp092xxxxxxx.top
X-RAY DIFFRACTION2water.paramwater.top

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