HEADER ENDOCYTOSIS 14-JAN-23 8I26 TITLE NMR STRUCTURE OF TOXOPLASMA GONDII PDCD5 (CIS FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROGRAMMED CELL DEATH 5 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TOXOPLASMA GONDII GT1; SOURCE 3 ORGANISM_TAXID: 507601; SOURCE 4 GENE: TGGT1_207690; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MOLTEN GLOBULE, HEPARAN SULFATE/HEPARIN BINDING PROTEIN, PROLINE CIS KEYWDS 2 FORM, ENDOCYTOSIS EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.H.LIN,C.H.HSU REVDAT 3 12-JUN-24 8I26 1 JRNL REVDAT 2 15-MAY-24 8I26 1 REMARK REVDAT 1 17-JAN-24 8I26 0 JRNL AUTH G.M.LIN,T.A.YU,C.F.CHANG,C.H.HSU JRNL TITL PROLINE ISOMERIZATION AND MOLTEN GLOBULAR PROPERTY OF JRNL TITL 2 TGPDCD5 SECRETED FROM TOXOPLASMA GONDII CONFERS ITS JRNL TITL 3 REGULATION OF HEPARIN SULFATE BINDING. JRNL REF JACS AU V. 4 1763 2024 JRNL REFN ESSN 2691-3704 JRNL PMID 38818051 JRNL DOI 10.1021/JACSAU.3C00577 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 8I26 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300031554. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 125 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN, 25 MM SODIUM PHOSPHATE, REMARK 210 100 MM SODIUM CHLORIDE, 10 MM REMARK 210 SODIUM AZIDE, 1 MM PMSF, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 2D 1H-15N HSQC; 3D 1H-13C REMARK 210 NOESY; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA, SPARKY REMARK 210 METHOD USED : DISTANCE GEOMETRY REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 PHE A 122 C PHE A 122 O -0.229 REMARK 500 2 PHE A 122 C PHE A 122 O -0.229 REMARK 500 3 PHE A 122 C PHE A 122 O -0.229 REMARK 500 4 PHE A 122 C PHE A 122 O -0.229 REMARK 500 5 PHE A 122 C PHE A 122 O -0.228 REMARK 500 6 PHE A 122 C PHE A 122 O -0.229 REMARK 500 7 PHE A 122 C PHE A 122 O -0.229 REMARK 500 8 PHE A 122 C PHE A 122 O -0.229 REMARK 500 9 PHE A 122 C PHE A 122 O -0.229 REMARK 500 10 PHE A 122 C PHE A 122 O -0.229 REMARK 500 11 PHE A 122 C PHE A 122 O -0.229 REMARK 500 12 PHE A 122 C PHE A 122 O -0.229 REMARK 500 13 PHE A 122 C PHE A 122 O -0.228 REMARK 500 14 PHE A 122 C PHE A 122 O -0.229 REMARK 500 15 PHE A 122 C PHE A 122 O -0.229 REMARK 500 16 PHE A 122 C PHE A 122 O -0.229 REMARK 500 17 PHE A 122 C PHE A 122 O -0.229 REMARK 500 18 PHE A 122 C PHE A 122 O -0.229 REMARK 500 19 PHE A 122 C PHE A 122 O -0.229 REMARK 500 20 PHE A 122 C PHE A 122 O -0.229 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 1 PHE A 122 CA - C - O ANGL. DEV. = 41.0 DEGREES REMARK 500 2 PHE A 122 CA - C - O ANGL. DEV. = 41.0 DEGREES REMARK 500 3 PHE A 122 CA - C - O ANGL. DEV. = 41.1 DEGREES REMARK 500 4 PHE A 122 CA - C - O ANGL. DEV. = 41.0 DEGREES REMARK 500 5 PHE A 122 CA - C - O ANGL. DEV. = 41.1 DEGREES REMARK 500 6 PHE A 122 CA - C - O ANGL. DEV. = 41.0 DEGREES REMARK 500 7 PHE A 122 CA - C - O ANGL. DEV. = 41.0 DEGREES REMARK 500 8 PHE A 122 CA - C - O ANGL. DEV. = 41.0 DEGREES REMARK 500 9 PHE A 122 CA - C - O ANGL. DEV. = 41.0 DEGREES REMARK 500 10 PHE A 122 CA - C - O ANGL. DEV. = 41.0 DEGREES REMARK 500 11 PHE A 122 CA - C - O ANGL. DEV. = 41.0 DEGREES REMARK 500 12 PHE A 122 CA - C - O ANGL. DEV. = 41.1 DEGREES REMARK 500 13 PHE A 122 CA - C - O ANGL. DEV. = 41.0 DEGREES REMARK 500 14 PHE A 122 CA - C - O ANGL. DEV. = 41.0 DEGREES REMARK 500 15 PHE A 122 CA - C - O ANGL. DEV. = 41.0 DEGREES REMARK 500 16 PHE A 122 CA - C - O ANGL. DEV. = 41.1 DEGREES REMARK 500 17 PHE A 122 CA - C - O ANGL. DEV. = 41.0 DEGREES REMARK 500 18 PHE A 122 CA - C - O ANGL. DEV. = 41.1 DEGREES REMARK 500 19 PHE A 122 CA - C - O ANGL. DEV. = 41.0 DEGREES REMARK 500 20 PHE A 122 CA - C - O ANGL. DEV. = 41.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 ALA A 7 -177.73 -58.82 REMARK 500 1 ARG A 11 67.15 60.63 REMARK 500 1 PHE A 14 -74.33 -153.65 REMARK 500 1 GLN A 33 86.09 44.65 REMARK 500 1 MET A 34 -178.11 -175.66 REMARK 500 1 GLU A 36 -77.13 -119.18 REMARK 500 1 ARG A 38 -63.32 -96.35 REMARK 500 1 VAL A 45 -74.91 -47.36 REMARK 500 1 THR A 47 141.86 -171.60 REMARK 500 1 PRO A 48 -165.29 -69.81 REMARK 500 1 GLU A 52 -74.32 -58.83 REMARK 500 1 ASN A 75 -57.45 -142.10 REMARK 500 1 ARG A 80 88.71 50.30 REMARK 500 1 ASP A 83 -62.77 -165.70 REMARK 500 1 LYS A 84 31.57 -95.13 REMARK 500 1 ASP A 86 179.36 -55.15 REMARK 500 1 THR A 97 81.19 172.99 REMARK 500 1 ALA A 99 -46.14 -140.77 REMARK 500 1 ALA A 100 116.42 -179.81 REMARK 500 1 SER A 101 -62.72 -171.63 REMARK 500 1 ALA A 102 172.85 68.42 REMARK 500 1 ALA A 103 149.19 67.30 REMARK 500 1 LYS A 104 -73.66 -139.51 REMARK 500 1 ASN A 105 32.32 -179.31 REMARK 500 1 THR A 106 159.78 172.67 REMARK 500 1 LYS A 108 44.99 31.27 REMARK 500 1 MET A 111 45.79 -84.87 REMARK 500 1 ARG A 112 100.25 71.60 REMARK 500 1 ARG A 113 106.44 68.42 REMARK 500 1 ARG A 114 -161.03 -74.27 REMARK 500 1 SER A 116 101.80 -51.55 REMARK 500 2 PHE A 6 34.32 -98.63 REMARK 500 2 ALA A 7 -178.31 -66.37 REMARK 500 2 ALA A 8 43.53 -84.22 REMARK 500 2 ALA A 9 91.22 52.85 REMARK 500 2 ARG A 11 64.04 63.27 REMARK 500 2 PHE A 14 -69.52 69.04 REMARK 500 2 GLN A 33 84.62 35.78 REMARK 500 2 GLU A 36 -76.93 -155.88 REMARK 500 2 ARG A 38 -64.03 -98.68 REMARK 500 2 THR A 47 122.25 179.09 REMARK 500 2 PRO A 48 -165.41 -69.73 REMARK 500 2 GLU A 52 -76.14 -52.25 REMARK 500 2 ASN A 75 -63.18 -135.51 REMARK 500 2 ARG A 80 96.75 56.90 REMARK 500 2 ASP A 83 -66.77 -167.47 REMARK 500 2 LYS A 84 34.02 -96.50 REMARK 500 2 VAL A 85 -178.55 -55.75 REMARK 500 2 ALA A 99 -59.20 -122.60 REMARK 500 2 ALA A 100 -38.37 -158.71 REMARK 500 REMARK 500 THIS ENTRY HAS 598 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 28099 RELATED DB: BMRB DBREF1 8I26 A 1 122 UNP A0A125YJ71_TOXGG DBREF2 8I26 A A0A125YJ71 1 122 SEQADV 8I26 SER A 0 UNP A0A125YJ7 EXPRESSION TAG SEQRES 1 A 123 SER MET GLN PRO GLU GLU PHE ALA ALA ALA ALA ARG GLY SEQRES 2 A 123 GLY PHE GLY GLY ASP ALA GLU LYS ALA LYS ALA ALA GLU SEQRES 3 A 123 ALA GLN GLU ALA MET ARG GLN GLN MET GLU GLU GLN ARG SEQRES 4 A 123 ARG ILE MET LEU ARG ALA VAL LEU THR PRO ALA ALA GLN SEQRES 5 A 123 GLU ARG LEU HIS ARG ILE GLN LEU VAL LYS ALA ASP LYS SEQRES 6 A 123 ALA ARG GLU VAL GLU ALA LEU ILE LEU GLN ASN ALA GLN SEQRES 7 A 123 ARG GLY ARG LEU ALA ASP LYS VAL ASP GLU ALA THR LEU SEQRES 8 A 123 ILE GLU LEU LEU GLN GLN THR SER ALA ALA SER ALA ALA SEQRES 9 A 123 LYS ASN THR PRO LYS VAL THR MET ARG ARG ARG PHE SER SEQRES 10 A 123 ASP ASP ASP ASP ASP PHE HELIX 1 AA1 ASP A 17 MET A 30 1 14 HELIX 2 AA2 ARG A 31 GLN A 33 5 3 HELIX 3 AA3 ARG A 38 VAL A 45 1 8 HELIX 4 AA4 ALA A 50 LYS A 61 1 12 HELIX 5 AA5 LYS A 61 LEU A 73 1 13 HELIX 6 AA6 GLU A 87 SER A 98 1 12 HELIX 7 AA7 SER A 116 ASP A 121 1 6 CISPEP 1 GLN A 2 PRO A 3 1 -0.03 CISPEP 2 THR A 106 PRO A 107 1 -0.07 CISPEP 3 GLN A 2 PRO A 3 2 -0.02 CISPEP 4 THR A 106 PRO A 107 2 -0.06 CISPEP 5 GLN A 2 PRO A 3 3 -0.02 CISPEP 6 THR A 106 PRO A 107 3 -0.10 CISPEP 7 GLN A 2 PRO A 3 4 0.03 CISPEP 8 THR A 106 PRO A 107 4 -0.03 CISPEP 9 GLN A 2 PRO A 3 5 -0.12 CISPEP 10 THR A 106 PRO A 107 5 -0.09 CISPEP 11 GLN A 2 PRO A 3 6 0.09 CISPEP 12 THR A 106 PRO A 107 6 -0.08 CISPEP 13 GLN A 2 PRO A 3 7 0.06 CISPEP 14 THR A 106 PRO A 107 7 -0.12 CISPEP 15 GLN A 2 PRO A 3 8 -0.12 CISPEP 16 THR A 106 PRO A 107 8 -0.04 CISPEP 17 GLN A 2 PRO A 3 9 -0.04 CISPEP 18 THR A 106 PRO A 107 9 -0.01 CISPEP 19 GLN A 2 PRO A 3 10 0.03 CISPEP 20 THR A 106 PRO A 107 10 -0.03 CISPEP 21 GLN A 2 PRO A 3 11 0.01 CISPEP 22 THR A 106 PRO A 107 11 -0.01 CISPEP 23 GLN A 2 PRO A 3 12 0.03 CISPEP 24 THR A 106 PRO A 107 12 -0.03 CISPEP 25 GLN A 2 PRO A 3 13 0.04 CISPEP 26 THR A 106 PRO A 107 13 -0.12 CISPEP 27 GLN A 2 PRO A 3 14 -0.01 CISPEP 28 THR A 106 PRO A 107 14 -0.02 CISPEP 29 GLN A 2 PRO A 3 15 0.02 CISPEP 30 THR A 106 PRO A 107 15 -0.06 CISPEP 31 GLN A 2 PRO A 3 16 -0.02 CISPEP 32 THR A 106 PRO A 107 16 -0.06 CISPEP 33 GLN A 2 PRO A 3 17 -0.01 CISPEP 34 THR A 106 PRO A 107 17 -0.02 CISPEP 35 GLN A 2 PRO A 3 18 0.00 CISPEP 36 THR A 106 PRO A 107 18 0.00 CISPEP 37 GLN A 2 PRO A 3 19 -0.04 CISPEP 38 THR A 106 PRO A 107 19 -0.06 CISPEP 39 GLN A 2 PRO A 3 20 0.02 CISPEP 40 THR A 106 PRO A 107 20 0.00 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 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 ENDMDL MODEL 2 ENDMDL MODEL 3 ENDMDL MODEL 4 ENDMDL MODEL 5 ENDMDL MODEL 6 ENDMDL MODEL 7 ENDMDL MODEL 8 ENDMDL MODEL 9 ENDMDL MODEL 10 ENDMDL MODEL 11 ENDMDL MODEL 12 ENDMDL MODEL 13 ENDMDL MODEL 14 ENDMDL MODEL 15 ENDMDL MODEL 16 ENDMDL MODEL 17 ENDMDL MODEL 18 ENDMDL MODEL 19 ENDMDL MODEL 20 ENDMDL MASTER 218 0 0 7 0 0 0 6 957 1 0 10 END