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- PDB-5std: SCYTALONE DEHYDRATASE PLUS INHIBITOR 2 -

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Basic information

Entry
Database: PDB / ID: 5std
TitleSCYTALONE DEHYDRATASE PLUS INHIBITOR 2
ComponentsScytalone dehydratase
KeywordsLYASE
Function / homology
Function and homology information


scytalone dehydratase / scytalone dehydratase activity / melanin biosynthetic process / endosome / metal ion binding
Similarity search - Function
Scytalone dehydratase / : / Scytalone dehydratase / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-UNN / Scytalone dehydratase
Similarity search - Component
Biological speciesMagnaporthe grisea (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWawrzak, Z. / Sandalova, T. / Steffens, J.J. / Basarab, G.S. / Lundqvist, T. / Lindqvist, Y. / Jordan, D.B.
CitationJournal: Proteins / Year: 1999
Title: High-resolution structures of scytalone dehydratase-inhibitor complexes crystallized at physiological pH.
Authors: Wawrzak, Z. / Sandalova, T. / Steffens, J.J. / Basarab, G.S. / Lundqvist, T. / Lindqvist, Y. / Jordan, D.B.
History
DepositionFeb 10, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 29, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 21, 2017Group: Advisory / Database references ...Advisory / Database references / Source and taxonomy / Structure summary
Category: entity / entity_name_com ...entity / entity_name_com / entity_src_gen / pdbx_distant_solvent_atoms / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num ..._entity.pdbx_description / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_seq_type / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code
Revision 1.4Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.5Sep 20, 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 / pdbx_struct_special_symmetry / struct_conn / 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.ptnr1_symmetry / _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_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Scytalone dehydratase
B: Scytalone dehydratase
C: Scytalone dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3749
Polymers58,1283
Non-polymers1,2466
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-34 kcal/mol
Surface area20090 Å2
MethodPISA
2
A: Scytalone dehydratase
B: Scytalone dehydratase
C: Scytalone dehydratase
hetero molecules

A: Scytalone dehydratase
B: Scytalone dehydratase
C: Scytalone dehydratase
hetero molecules

A: Scytalone dehydratase
B: Scytalone dehydratase
C: Scytalone dehydratase
hetero molecules

A: Scytalone dehydratase
B: Scytalone dehydratase
C: Scytalone dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,49736
Polymers232,51112
Non-polymers4,98624
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area36980 Å2
ΔGint-266 kcal/mol
Surface area77920 Å2
MethodPISA
3
A: Scytalone dehydratase
B: Scytalone dehydratase
C: Scytalone dehydratase
hetero molecules

A: Scytalone dehydratase
B: Scytalone dehydratase
C: Scytalone dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,74818
Polymers116,2556
Non-polymers2,49312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area18210 Å2
ΔGint-76 kcal/mol
Surface area38900 Å2
MethodPISA
4
A: Scytalone dehydratase
B: Scytalone dehydratase
C: Scytalone dehydratase
hetero molecules

A: Scytalone dehydratase
B: Scytalone dehydratase
C: Scytalone dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,74818
Polymers116,2556
Non-polymers2,49312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area17590 Å2
ΔGint-104 kcal/mol
Surface area39680 Å2
MethodPISA
5
A: Scytalone dehydratase
B: Scytalone dehydratase
C: Scytalone dehydratase
hetero molecules

A: Scytalone dehydratase
B: Scytalone dehydratase
C: Scytalone dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,74818
Polymers116,2556
Non-polymers2,49312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area17430 Å2
ΔGint-102 kcal/mol
Surface area39850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.620, 92.290, 164.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-501-

CA

21B-502-

CA

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Components

#1: Protein Scytalone dehydratase / SDH


Mass: 19375.893 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe grisea (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: P56221, scytalone dehydratase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-UNN / (6,7-DIFLUORO-QUINAZOLIN-4-YL)-(1-METHYL-2,2-DIPHENYL-ETHYL)-AMINE


Mass: 375.414 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C23H19F2N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1200 mM1reservoirCaCl2
234 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 47813 / % possible obs: 92.9 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 18.5
Reflection shellHighest resolution: 1.95 Å / % possible all: 85.5
Reflection
*PLUS
Num. measured all: 424274
Reflection shell
*PLUS
% possible obs: 85.5 %

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Processing

Software
NameClassification
AMoREphasing
X-PLORrefinement
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1STD

1std


Resolution: 1.95→20 Å / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.259 -7.5 %RANDOM
Rwork0.212 ---
obs-424274 92.9 %-
Displacement parametersBiso mean: 23.9 Å2
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4104 0 87 239 4430
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.686
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.07
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.206
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 44250 / σ(F): 2 / % reflection Rfree: 7.5 % / Rfactor obs: 0.212
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 23.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.07
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.206

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