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- PDB-1zco: Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino-heptul... -

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Basic information

Entry
Database: PDB / ID: 1zco
TitleCrystal structure of pyrococcus furiosus 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase
Components2-dehydro-3-deoxyphosphoheptonate aldolase
KeywordsLYASE / arabino-heptulosonate / synthase / shikimate / DAHP / DAH7P / DAHPS / DAH7PS
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aldehyde-lyase activity / aromatic amino acid family biosynthetic process / metal ion binding
Similarity search - Function
Phospho-2-dehydro-3-deoxyheptonate aldolase, subtype 2 / : / 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 / 2-dehydro-3-deoxyphosphoheptonate aldolase
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsSchofield, L.R. / Anderson, B.F. / Patchett, M.L. / Norris, G.E. / Jameson, G.B. / Parker, E.J.
Citation
Journal: Biochemistry / Year: 2005
Title: Substrate Ambiguity and Crystal Structure of Pyrococcus furiosus 3-Deoxy-d-arabino-heptulosonate-7-phosphate Synthase: An Ancestral 3-Deoxyald-2-ulosonate-phosphate Synthase?(,)
Authors: Schofield, L.R. / Anderson, B.F. / Patchett, M.L. / Norris, G.E. / Jameson, G.B. / Parker, E.J.
#1: Journal: PROTEIN EXPR.PURIF. / Year: 2004
Title: Expression, Purification, and Characteriseation of 3-Deoxy_D_Arabino_Heptulosonate 7-Phosphate Synthase from Pyrococcus Furiosus
Authors: Schofield, L.R. / Patchett, M.L. / Parker, E.J.
History
DepositionApr 12, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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 / 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_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_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-deoxyphosphoheptonate aldolase
B: 2-dehydro-3-deoxyphosphoheptonate aldolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,9837
Polymers58,5212
Non-polymers4625
Water4,720262
1
A: 2-dehydro-3-deoxyphosphoheptonate aldolase
B: 2-dehydro-3-deoxyphosphoheptonate aldolase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)117,96614
Polymers117,0434
Non-polymers92410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area13610 Å2
ΔGint-135 kcal/mol
Surface area32800 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)87.231, 110.024, 144.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological tetramer can be generated by the operation of the crystallographic twofold axis 1-x,y,-z on the asymmetric unit

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Components

#1: Protein 2-dehydro-3-deoxyphosphoheptonate aldolase / DAH7PS / 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase


Mass: 29260.646 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Plasmid: PT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CODONPLUS(DE3)-RIL / References: UniProt: Q8U0A9, EC: 4.1.2.15
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE


Mass: 168.042 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O6P
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 262 / 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: 3 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 8% Peg 8000, 0.2M ammonium acetate, 0.1M tris-HCl, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 7, 2004 / Details: Osmic Blue Mirrors
RadiationMonochromator: OSMIC BLUE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→19.8 Å / Num. all: 166567 / Num. obs: 33241 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.97 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 7.6
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 4.97 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
CrystalCleardata collection
CrystalCleardata reduction
MOLREPphasing
REFMAC5.1.24refinement
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CHIMERIC MODEL FROM 1QR7 AND 1FWT

1qr7

1fwt


Resolution: 2.25→19.8 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.098 / SU ML: 0.163 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.245 / ESU R Free: 0.203 / Stereochemistry target values: Supplied by CCP4 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23132 2519 7.6 %RANDOM
Rwork0.18224 ---
obs0.186 30722 100 %-
all-30722 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.545 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--1.72 Å20 Å2
3----2.17 Å2
Refine analyzeLuzzati coordinate error obs: 0.316 Å / Luzzati d res low obs: 4.8 Å
Refinement stepCycle: LAST / Resolution: 2.25→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4112 0 23 262 4397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0224221
X-RAY DIFFRACTIONr_bond_other_d0.0010.023934
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.9785701
X-RAY DIFFRACTIONr_angle_other_deg1.56239171
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6545524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024641
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02813
X-RAY DIFFRACTIONr_nbd_refined0.2420.2864
X-RAY DIFFRACTIONr_nbd_other0.2570.24666
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0850.22515
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2130.2222
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.296
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2640.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.61332611
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.69354213
X-RAY DIFFRACTIONr_scbond_it3.6861610
X-RAY DIFFRACTIONr_scangle_it5.40581488
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.338 162
Rwork0.276 2232
obs-2232

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