HEADER FLUORESCENT PROTEIN 08-AUG-22 8AO0
TITLE SOLUTION STRUCTURE OF NANOFAST/HBR-DOM2 COMPLEX
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PHOTOACTIVE YELLOW PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: PYP;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT;
SOURCE 3 ORGANISM_TAXID: 32630;
SOURCE 4 GENE: PYP;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS FLUOROGEN-ACTIVATING PROTEIN, FAST, NANOFAST, SPATIAL STRUCTURE,
KEYWDS 2 DYNAMICS, LIGAND SEPCIFICITY, FLUOROGEN, BINDING CONSTATNT,
KEYWDS 3 FLUORESCENT PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR V.A.LUSHPA,M.V.GONCHARUK,S.A.GONCHARUK,N.S.BALEEVA,M.S.BARANOV,
AUTHOR 2 K.S.MINEEV
REVDAT 2 23-OCT-24 8AO0 1 REMARK
REVDAT 1 23-NOV-22 8AO0 0
JRNL AUTH V.A.LUSHPA,N.S.BALEEVA,S.A.GONCHARUK,M.V.GONCHARUK,
JRNL AUTH 2 A.S.ARSENIEV,M.S.BARANOV,K.S.MINEEV
JRNL TITL SPATIAL STRUCTURE OF NANOFAST IN THE APO STATE AND IN
JRNL TITL 2 COMPLEX WITH ITS FLUOROGEN HBR-DOM2.
JRNL REF INT J MOL SCI V. 23 2022
JRNL REFN ESSN 1422-0067
JRNL PMID 36232662
JRNL DOI 10.3390/IJMS231911361
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CYANA 3.98.13
REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 8AO0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-AUG-22.
REMARK 100 THE DEPOSITION ID IS D_1292124780.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 7.0
REMARK 210 IONIC STRENGTH : NULL
REMARK 210 PRESSURE : AMBIENT PA
REMARK 210 SAMPLE CONTENTS : 20 MM NAPI, 20 MM SODIUM
REMARK 210 CHLORIDE, 0.001 % SODIUM AZIDE,
REMARK 210 90% H2O/10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC
REMARK 210 ALIPHATIC; 2D 1H-13C HSQC
REMARK 210 AROMATIC; 3D HNCO; 3D HNCA; 3D
REMARK 210 HN(CO)CA; 3D HNCACO; 3D TOCSY;
REMARK 210 3D HCCH-COSY; 3D HCCH-TOCSY; 3D
REMARK 210 1H-13C NOESY; 3D 1H-15N NOESY;
REMARK 210 3D HNCACB; HBCBCARHAR
REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE III
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : TOPSPIN 3.0, QMDD 3.2, CARA
REMARK 210 1.9.1.7
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 100
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20
REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST
REMARK 210 RESTRAINT VIOLATIONS
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: NULL
REMARK 215
REMARK 215 NMR STUDY
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION
REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON
REMARK 215 THESE RECORDS ARE MEANINGLESS.
REMARK 300
REMARK 300 BIOMOLECULE: 1
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON
REMARK 300 BURIED SURFACE AREA.
REMARK 350
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS
REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.
REMARK 350
REMARK 350 BIOMOLECULE: 1
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A
REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 1 ASP A 39 -71.51 -89.71
REMARK 500 1 ASP A 45 97.37 -59.25
REMARK 500 1 PHE A 49 -71.12 -96.86
REMARK 500 1 ASN A 61 84.14 179.84
REMARK 500 1 ASP A 90 35.85 -142.01
REMARK 500 1 ALA A 102 103.70 -54.94
REMARK 500 1 HIS A 109 171.92 -55.17
REMARK 500 2 ASP A 39 -71.61 -90.80
REMARK 500 2 ASP A 45 97.82 -59.35
REMARK 500 2 PHE A 49 -68.92 -96.38
REMARK 500 2 ASN A 61 86.09 179.73
REMARK 500 2 ALA A 104 109.46 -172.26
REMARK 500 2 HIS A 109 -59.56 -127.72
REMARK 500 3 ASP A 39 -71.65 -90.07
REMARK 500 3 ASP A 45 97.10 -59.11
REMARK 500 3 PHE A 49 -71.67 -95.81
REMARK 500 3 ASN A 61 90.32 179.16
REMARK 500 3 ALA A 86 172.27 -56.04
REMARK 500 3 VAL A 99 176.29 -56.68
REMARK 500 3 ALA A 103 -75.28 -103.68
REMARK 500 4 ASP A 39 -71.28 -91.34
REMARK 500 4 ASP A 45 96.77 -59.35
REMARK 500 4 PHE A 49 -69.20 -95.37
REMARK 500 4 ASN A 61 83.82 179.51
REMARK 500 4 ASP A 90 35.97 -143.39
REMARK 500 4 VAL A 99 -179.73 -63.96
REMARK 500 5 ASP A 39 -71.59 -89.91
REMARK 500 5 ASP A 45 97.49 -59.10
REMARK 500 5 PHE A 49 -68.74 -95.63
REMARK 500 5 ASN A 61 81.17 -179.96
REMARK 500 6 ASP A 39 -71.54 -88.75
REMARK 500 6 ASP A 45 96.88 -59.24
REMARK 500 6 PHE A 49 -70.90 -99.27
REMARK 500 6 ASN A 61 87.07 179.03
REMARK 500 6 SER A 91 -175.73 -179.76
REMARK 500 7 ASP A 39 -71.35 -91.78
REMARK 500 7 ASP A 45 97.30 -59.04
REMARK 500 7 PHE A 49 -68.42 -94.45
REMARK 500 7 ASN A 61 84.54 179.42
REMARK 500 7 ALA A 104 -174.89 -60.53
REMARK 500 8 ASP A 39 -71.58 -80.84
REMARK 500 8 ASP A 45 97.41 -59.43
REMARK 500 8 PHE A 49 -69.29 -96.35
REMARK 500 8 ASN A 61 84.46 179.39
REMARK 500 8 GLU A 106 41.55 -104.60
REMARK 500 9 ASP A 39 -71.24 -79.68
REMARK 500 9 ASP A 45 97.15 -59.62
REMARK 500 9 PHE A 49 -69.35 -97.40
REMARK 500 9 ASN A 61 85.37 179.85
REMARK 500 10 ASP A 39 -71.55 -89.70
REMARK 500
REMARK 500 THIS ENTRY HAS 120 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 34746 RELATED DB: BMRB
REMARK 900 SOLUTION STRUCTURE OF NANOFAST/HBR-DOM2 COMPLEX
DBREF 8AO0 A 2 99 UNP P16113 PYP_HALHA 28 125
SEQADV 8AO0 MET A 1 UNP P16113 INITIATING METHIONINE
SEQADV 8AO0 GGL A 20 UNP P16113 GLU 46 CONFLICT
SEQADV 8AO0 GLY A 43 UNP P16113 CYS 69 CONFLICT
SEQADV 8AO0 TRP A 68 UNP P16113 TYR 94 CONFLICT
SEQADV 8AO0 MET A 69 UNP P16113 THR 95 CONFLICT
SEQADV 8AO0 ILE A 70 UNP P16113 PHE 96 CONFLICT
SEQADV 8AO0 PRO A 71 UNP P16113 ASP 97 CONFLICT
SEQADV 8AO0 THR A 72 UNP P16113 TYR 98 CONFLICT
SEQADV 8AO0 SER A 73 UNP P16113 GLN 99 CONFLICT
SEQADV 8AO0 ARG A 74 UNP P16113 MET 100 CONFLICT
SEQADV 8AO0 GLY A 75 UNP P16113 THR 101 CONFLICT
SEQADV 8AO0 LYS A 100 UNP P16113 EXPRESSION TAG
SEQADV 8AO0 LEU A 101 UNP P16113 EXPRESSION TAG
SEQADV 8AO0 ALA A 102 UNP P16113 EXPRESSION TAG
SEQADV 8AO0 ALA A 103 UNP P16113 EXPRESSION TAG
SEQADV 8AO0 ALA A 104 UNP P16113 EXPRESSION TAG
SEQADV 8AO0 LEU A 105 UNP P16113 EXPRESSION TAG
SEQADV 8AO0 GLU A 106 UNP P16113 EXPRESSION TAG
SEQADV 8AO0 HIS A 107 UNP P16113 EXPRESSION TAG
SEQADV 8AO0 HIS A 108 UNP P16113 EXPRESSION TAG
SEQADV 8AO0 HIS A 109 UNP P16113 EXPRESSION TAG
SEQADV 8AO0 HIS A 110 UNP P16113 EXPRESSION TAG
SEQADV 8AO0 HIS A 111 UNP P16113 EXPRESSION TAG
SEQADV 8AO0 HIS A 112 UNP P16113 EXPRESSION TAG
SEQRES 1 A 112 MET PHE GLY ALA ILE GLN LEU ASP GLY ASP GLY ASN ILE
SEQRES 2 A 112 LEU GLN TYR ASN ALA ALA GGL GLY ASP ILE THR GLY ARG
SEQRES 3 A 112 ASP PRO LYS GLN VAL ILE GLY LYS ASN PHE PHE LYS ASP
SEQRES 4 A 112 VAL ALA PRO GLY THR ASP SER PRO GLU PHE TYR GLY LYS
SEQRES 5 A 112 PHE LYS GLU GLY VAL ALA SER GLY ASN LEU ASN THR MET
SEQRES 6 A 112 PHE GLU TRP MET ILE PRO THR SER ARG GLY PRO THR LYS
SEQRES 7 A 112 VAL LYS VAL HIS MET LYS LYS ALA LEU SER GLY ASP SER
SEQRES 8 A 112 TYR TRP VAL PHE VAL LYS ARG VAL LYS LEU ALA ALA ALA
SEQRES 9 A 112 LEU GLU HIS HIS HIS HIS HIS HIS
HET GGL A 20 16
HET O1F A 201 29
HETNAM GGL GAMMA-L-GLUTAMIC ACID
HETNAM O1F (5~{Z})-5-[(2,5-DIMETHOXY-4-OXIDANYL-PHENYL)
HETNAM 2 O1F METHYLIDENE]-2-SULFANYLIDENE-1,3-THIAZOLIDIN-4-ONE
HETSYN GGL L-GLUTAMIC ACID
FORMUL 1 GGL C5 H9 N O4
FORMUL 2 O1F C12 H11 N O4 S2
HELIX 1 AA1 ASN A 17 GLY A 25 1 9
HELIX 2 AA2 ASP A 27 ILE A 32 1 6
HELIX 3 AA3 PHE A 49 GLY A 60 1 12
SHEET 1 AA1 5 ILE A 13 TYR A 16 0
SHEET 2 AA1 5 GLY A 3 LEU A 7 -1 N GLN A 6 O LEU A 14
SHEET 3 AA1 5 TYR A 92 ARG A 98 -1 O TYR A 92 N LEU A 7
SHEET 4 AA1 5 GLY A 75 LYS A 85 -1 N LYS A 80 O LYS A 97
SHEET 5 AA1 5 ASN A 63 THR A 72 -1 N TRP A 68 O VAL A 79
LINK C ALA A 19 N GGL A 20 1555 1555 1.33
LINK C GGL A 20 N GLY A 21 1555 1555 1.33
CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1
ORIGX1 1.000000 0.000000 0.000000 0.00000
ORIGX2 0.000000 1.000000 0.000000 0.00000
ORIGX3 0.000000 0.000000 1.000000 0.00000
SCALE1 1.000000 0.000000 0.000000 0.00000
SCALE2 0.000000 1.000000 0.000000 0.00000
SCALE3 0.000000 0.000000 1.000000 0.00000
MODEL 1