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- PDB-1ofr: CRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEP... -

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Entry
Database: PDB / ID: 1ofr
TitleCRYSTAL STRUCTURE OF THE TYROSINE-REGULATED 3-DEOXY-D-ARABINO-HEPTULOSONATE-7-PHOSPHATE SYNTHASE FROM SACCHAROMYCES CEREVISIAE COMPLEXED WITH PHENYLALANINE AND MANGANESE
ComponentsPHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
KeywordsLYASE / BETA-ALPHA-BARREL / AROMATIC AMINO-ACID BIOSYNTHESIS
Function / homology
Function and homology information


3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / nucleus / cytoplasm
Similarity search - Function
DAHP synthase, class 1 / 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
: / PHENYLALANINE / Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited
Similarity search - Component
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsKoenig, V. / Pfeil, A. / Heinrich, G. / Braus, G. / Schneider, T.R.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Substrate and Metal Complexes of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase from Saccharomyces Cerevisiae Provide New Insights Into the Catalytic Mechanism.
Authors: Koenig, V. / Pfeil, A. / Heinrich, G. / Braus, G. / Schneider, T.R.
History
DepositionApr 18, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_asym_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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "GB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "HA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 7-STRANDED BARREL THIS IS REPRESENTED BY A 8-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
B: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
C: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
D: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
E: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
F: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
G: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
H: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)319,47720
Polymers318,3768
Non-polymers1,10012
Water57632
1
A: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
B: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7044
Polymers79,5942
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
D: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0346
Polymers79,5942
Non-polymers4404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
F: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7044
Polymers79,5942
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
H: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0346
Polymers79,5942
Non-polymers4404
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
E: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
F: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
G: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
H: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,73810
Polymers159,1884
Non-polymers5506
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14230 Å2
ΔGint-89.09 kcal/mol
Surface area46660 Å2
MethodPISA
6
A: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
B: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
C: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
D: PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,73810
Polymers159,1884
Non-polymers5506
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14540 Å2
ΔGint-83.58 kcal/mol
Surface area47420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.287, 94.034, 105.121
Angle α, β, γ (deg.)65.14, 85.68, 75.73
Int Tables number1
Space group name H-MP1
DetailsTHE 8 MOLECULES CONTAINED IN THE ASSYMETRIC UNIT AREARRANGED IN TWO TETRAMERS (DIMER OF DIMERS) WITH APPROXIMATE 222 POINT SYMMETRY. THE TETRAMERS HAVE VERY SIMILAR ORIENTATIONS,WITH THEIR CENTERS OF MASS BEING RELATED BY A CRYSTALLOGRAPHIC TRANSLATION OF (0.5,0.5,0)

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Components

#1: Protein
PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE / PHOSPHO-2-KETO-3-DEOXYHEPTONATE ALDOLASE DAHP SYNTHETASE / 3-DEOXY-D-ARABINO-HEPTULOSONATE 7- ...PHOSPHO-2-KETO-3-DEOXYHEPTONATE ALDOLASE DAHP SYNTHETASE / 3-DEOXY-D-ARABINO-HEPTULOSONATE 7-PHOSPHATE SYNTHASE / PHOSPHO-2-DEHYDRO- 3-DEOXYHEPTONATE ALDOLASE


Mass: 39797.055 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: LIGANDS ARE PHENYLALANINE ION, MANGANESE
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Strain: RH1326 / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P32449, EC: 4.1.2.15
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-PHE / PHENYLALANINE


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: 2-DEHYDRO-3-DEOXY-D-ARABINO-HEPTONATE 7- PHOSPHATE + PHOSPHATE = ...CATALYTIC ACTIVITY: 2-DEHYDRO-3-DEOXY-D-ARABINO-HEPTONATE 7- PHOSPHATE + PHOSPHATE = PHOSPHOENOLPYRUVATE + D-ERYTHROSE 4- PHOSPHATE + 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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growpH: 8 / Details: pH 8.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8463
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 2002 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8463 Å / Relative weight: 1
ReflectionResolution: 2.7→37 Å / Num. obs: 155910 / % possible obs: 91.2 % / Redundancy: 2.1 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.8
Reflection shellResolution: 2.69→2.8 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3.5 / % possible all: 78.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: MOLECULE A OF PDB-CODE 1HFB

1hfb


Resolution: 2.7→37.2 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 813855.17 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE EFFECTOR PHENYLALANINE IS MODELLED ONLY IN THE FOUR MOLECULES C, D, G, H
RfactorNum. reflection% reflectionSelection details
Rfree0.274 3373 5.2 %RANDOM
Rwork0.232 ---
obs0.232 65376 85.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 18.0698 Å2 / ksol: 0.2985 e/Å3
Displacement parametersBiso mean: 48.6 Å2
Baniso -1Baniso -2Baniso -3
1-4.33 Å2-7.4 Å2-0.22 Å2
2--5.08 Å21.42 Å2
3----9.41 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.41 Å
Luzzati d res low-5 Å
Luzzati sigma a0.7 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 2.7→37.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20842 0 56 32 20930
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.861.5
X-RAY DIFFRACTIONc_mcangle_it3.132
X-RAY DIFFRACTIONc_scbond_it2.582
X-RAY DIFFRACTIONc_scangle_it3.972.5
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.434 529 6.4 %
Rwork0.427 7788 -
obs--65.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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