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- PDB-4woj: Aspartate Semialdehyde Dehydrogenase from Francisella tularensis -

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Basic information

Entry
Database: PDB / ID: 4woj
TitleAspartate Semialdehyde Dehydrogenase from Francisella tularensis
ComponentsAspartate semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Lysine Biosynthesis / Oligomerization / Dimerization
Function / homology
Function and homology information


aspartate-semialdehyde dehydrogenase / aspartate-semialdehyde dehydrogenase activity / threonine biosynthetic process / methionine biosynthetic process / isoleucine biosynthetic process / lysine biosynthetic process via diaminopimelate / NAD binding / NADP binding / protein dimerization activity
Similarity search - Function
Aspartate-semialdehyde dehydrogenase, gamma-type / Aspartate-semialdehyde dehydrogenase, conserved site / Aspartate-semialdehyde dehydrogenase signature. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 ...Aspartate-semialdehyde dehydrogenase, gamma-type / Aspartate-semialdehyde dehydrogenase, conserved site / Aspartate-semialdehyde dehydrogenase signature. / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, dimerisation domain / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aspartate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesFrancisella tularensis subsp. tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsMank, N.J. / Arnette, A.K. / Klapper, V.G. / Chruszcz, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2018
Title: Structure of aspartate b-semialdehyde dehydrogenase from Francisella tularensis
Authors: Mank, N.J. / Pote, S. / Majorek, K.A. / Arnette, A.K. / Klapper, V.G. / Hurlburt, B.K. / Chruszcz, M.
History
DepositionOct 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 2.0Jan 17, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site_gen
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _atom_site.label_seq_id / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_ec / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_label_seq_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.label_seq_id
Revision 2.1Sep 27, 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_ncs_dom_lim
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_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_symmetry / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aspartate semialdehyde dehydrogenase
B: Aspartate semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1506
Polymers82,8392
Non-polymers3114
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-79 kcal/mol
Surface area27370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.587, 60.573, 67.684
Angle α, β, γ (deg.)115.430, 100.980, 91.740
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 1 - 363 / Label seq-ID: 7 - 369

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Aspartate semialdehyde dehydrogenase


Mass: 41419.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis subsp. tularensis (bacteria)
Gene: asd / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8G8T7
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.07 Å3/Da / Density % sol: 40.45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 28, 2014
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.45→40 Å / Num. all: 23498 / Num. obs: 23498 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.054 / Rrim(I) all: 0.076 / Rsym value: 0.054 / Χ2: 1.254 / Net I/av σ(I): 16.887 / Net I/σ(I): 13.7 / Num. measured all: 45447
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.45-2.491.80.2013.311380.9050.2010.2840.87294.3
2.49-2.541.90.20711400.9160.2070.2920.96495.6
2.54-2.591.90.17611900.9480.1760.2491.00696.6
2.59-2.641.90.16611680.9450.1660.2350.96197.5
2.64-2.71.90.16311540.9490.1630.230.99297.3
2.7-2.761.90.1412280.9680.140.1980.98997.5
2.76-2.831.90.13911260.9540.1390.1961.04598.1
2.83-2.91.90.11912210.9660.1190.1691.01998.2
2.9-2.9920.10711900.9730.1070.1521.09197.9
2.99-3.0920.09711700.9730.0970.1381.17498.7
3.09-3.220.0811670.9840.080.1141.07498.1
3.2-3.3220.06211930.990.0620.0881.13598.3
3.32-3.4820.05411720.9910.0540.0761.31798.4
3.48-3.6620.04611990.9940.0460.0651.36198.5
3.66-3.8920.0412150.9950.040.0561.37398.2
3.89-4.191.90.03511600.9960.0350.0491.3598.1
4.19-4.611.90.02911910.9970.0290.0411.29798.3
4.61-5.2720.03211920.9960.0320.0451.51398.8
5.27-6.641.90.03711860.9930.0370.0531.44598.8
6.64-401.90.04310980.9910.0430.0613.14990.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data collection
HKL-3000data scaling
HKL-2000data scaling
MOLREPphasing
REFMAC5.7.0029refinement
Cootmodel building
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1T4B

1t4b


Resolution: 2.45→37.22 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.842 / SU ML: 0.244 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2376 1180 5.1 %RANDOM
Rwork0.1834 22134 --
obs0.1863 22134 97.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 112.63 Å2 / Biso mean: 37.408 Å2 / Biso min: 5.54 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å21.57 Å2-2.15 Å2
2--4.78 Å2-0.21 Å2
3----1.38 Å2
Refinement stepCycle: final / Resolution: 2.45→37.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5653 0 16 112 5781
Biso mean--88.65 29.12 -
Num. residues----729
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0195771
X-RAY DIFFRACTIONr_bond_other_d0.0060.025627
X-RAY DIFFRACTIONr_angle_refined_deg1.5261.9717814
X-RAY DIFFRACTIONr_angle_other_deg1.01312968
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2025731
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.75225.602241
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.015151071
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6971525
X-RAY DIFFRACTIONr_chiral_restr0.0870.2916
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026486
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021227
Refine LS restraints NCS

Ens-ID: 1 / Number: 22451 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 89 -
Rwork0.249 1584 -
all-1673 -
obs--94.52 %

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